R Notebook
Last updated: 2019-01-01
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library(dplyr)
Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionlibrary(Seurat)Loading required package: ggplot2Loading required package: cowplot
Attaching package: 'cowplot'The following object is masked from 'package:ggplot2':
ggsaveLoading required package: Matrixlibrary(gProfileR)all10x <- readRDS('output/10x-180504')One cluster in the data contains cells from all samples
TSNEPlot(all10x, group.by='sample_name', pt.size=0.1)
Cluster 12
TSNEPlot(all10x, group.by='res.0.5', pt.size=0.1, do.label=T)
Marker genes
markers <- read.table('output/markergenes/180504/markers_10x-180504_res.0.5_negbinom', sep='\t', header=T)
mixture <- markers[markers$cluster == 12,]
mixture <- mixture[mixture$p_val_adj < 0.05,]
mixture_pos <- mixture[order(-mixture$avg_logFC),]
mixture_neg <- mixture[order(mixture$avg_logFC),]Positive markers
as.data.frame(mixture_pos) cluster p_val avg_logFC pct.1 pct.2 p_val_adj
2049 12 0.000000e+00 1.3327502 0.895 0.895 0.000000e+00
2255 12 8.614404e-235 1.2978399 1.000 1.000 2.074176e-230
2846 12 3.547151e-94 1.1430022 0.998 0.993 8.540829e-90
2608 12 6.905506e-140 1.1026415 1.000 0.999 1.662708e-135
2625 12 1.764444e-136 1.0859023 0.991 0.992 4.248428e-132
2812 12 1.189038e-101 0.9816995 0.996 0.968 2.862965e-97
2919 12 2.029038e-57 0.9742187 0.943 0.923 4.885517e-53
2813 12 1.497577e-101 0.9649495 1.000 0.987 3.605866e-97
2598 12 1.921461e-143 0.9514433 0.947 0.994 4.626494e-139
2910 12 3.887985e-65 0.9424130 0.999 0.989 9.361489e-61
2753 12 5.892383e-116 0.9223137 0.996 0.972 1.418768e-111
2912 12 1.982561e-62 0.9188733 0.990 0.956 4.773612e-58
2202 12 4.479297e-276 0.8987640 0.755 0.635 1.078525e-271
2891 12 6.932459e-81 0.8911547 0.972 0.936 1.669197e-76
2892 12 6.892859e-79 0.8757626 0.988 0.950 1.659663e-74
2942 12 3.926200e-39 0.8751378 0.999 0.999 9.453504e-35
2633 12 1.988425e-135 0.8709833 0.989 0.957 4.787729e-131
2977 12 1.187346e-28 0.8673550 0.986 0.975 2.858892e-24
2941 12 1.063143e-40 0.8551415 0.999 1.000 2.559835e-36
2893 12 1.082714e-77 0.8514443 1.000 0.998 2.606959e-73
2904 12 4.623468e-71 0.8486577 0.996 0.992 1.113239e-66
2807 12 1.161964e-102 0.8469319 0.946 0.869 2.797777e-98
2804 12 3.359547e-103 0.8326101 0.957 0.891 8.089116e-99
2937 12 3.802018e-44 0.8307130 0.996 0.996 9.154500e-40
2999 12 7.364136e-24 0.8062394 0.896 0.856 1.773137e-19
3138 12 2.683866e-07 0.8035485 0.996 0.980 6.462212e-03
2994 12 2.611599e-25 0.7905585 1.000 1.000 6.288208e-21
2934 12 8.759269e-47 0.7815058 0.987 0.982 2.109057e-42
2867 12 2.086724e-87 0.7792938 0.975 0.923 5.024414e-83
2958 12 9.505189e-33 0.7785246 1.000 1.000 2.288659e-28
2915 12 8.407361e-62 0.7699642 0.975 0.934 2.024324e-57
3116 12 2.214225e-09 0.7517954 0.995 0.975 5.331410e-05
2983 12 2.113612e-27 0.7468260 0.991 0.980 5.089154e-23
2962 12 4.484064e-32 0.7363554 0.997 0.992 1.079673e-27
2933 12 1.475592e-47 0.7234454 0.940 0.829 3.552929e-43
2976 12 9.166893e-29 0.7229113 0.993 0.989 2.207205e-24
2951 12 6.884296e-35 0.7222543 0.989 0.973 1.657601e-30
2917 12 8.428734e-60 0.7186755 0.920 0.947 2.029471e-55
2938 12 5.483953e-44 0.7110705 0.981 0.943 1.320426e-39
3059 12 1.426291e-14 0.7078997 0.997 1.000 3.434223e-10
2940 12 9.058510e-41 0.7076955 0.995 0.992 2.181108e-36
3051 12 2.029214e-15 0.6995125 1.000 1.000 4.885941e-11
3058 12 8.209677e-15 0.6923497 0.921 0.839 1.976726e-10
3019 12 3.456933e-20 0.6852300 0.969 0.949 8.323604e-16
2916 12 1.107699e-60 0.6830628 0.795 0.891 2.667118e-56
2918 12 6.388973e-59 0.6789562 0.764 0.762 1.538337e-54
2960 12 1.811726e-32 0.6779660 0.917 0.833 4.362275e-28
3028 12 1.130948e-18 0.6663717 0.965 0.945 2.723095e-14
2973 12 6.812614e-30 0.6655060 0.968 0.938 1.640341e-25
2995 12 2.732381e-25 0.6649891 0.981 0.937 6.579028e-21
3148 12 1.635820e-06 0.6635402 0.993 0.961 3.938726e-02
2968 12 2.287010e-31 0.6594054 0.946 0.841 5.506664e-27
3134 12 2.069039e-07 0.6590033 0.996 0.986 4.981832e-03
3129 12 1.602184e-07 0.6581014 0.998 0.998 3.857739e-03
3018 12 2.750064e-20 0.6572799 0.979 0.935 6.621605e-16
3070 12 6.429362e-14 0.6525017 0.999 0.996 1.548062e-09
3044 12 7.562375e-16 0.6506241 0.981 0.984 1.820869e-11
2978 12 2.268224e-28 0.6460210 0.966 0.947 5.461429e-24
2900 12 3.393774e-75 0.6361930 0.824 0.653 8.171529e-71
3039 12 4.789789e-16 0.6168885 0.983 0.962 1.153285e-11
2935 12 1.077740e-46 0.6127951 0.874 0.834 2.594982e-42
2932 12 9.820720e-48 0.6099372 0.858 0.758 2.364633e-43
2986 12 1.402561e-26 0.6092847 0.911 0.833 3.377087e-22
2997 12 3.896657e-24 0.6091090 0.888 0.916 9.382372e-20
3103 12 2.066554e-10 0.6086655 0.999 0.994 4.975849e-06
2992 12 1.575472e-25 0.6083947 0.939 0.880 3.793421e-21
3112 12 8.748348e-10 0.6045117 0.862 0.884 2.106427e-05
3036 12 4.762223e-17 0.6042620 0.968 0.930 1.146648e-12
3073 12 1.642908e-13 0.6029394 0.981 0.958 3.955795e-09
2988 12 2.140507e-26 0.6010164 0.898 0.898 5.153914e-22
3046 12 1.341752e-15 0.5960556 0.993 0.987 3.230670e-11
2936 12 4.843083e-46 0.5882979 0.878 0.784 1.166118e-41
3087 12 1.377813e-11 0.5844032 0.961 0.951 3.317498e-07
2926 12 2.864088e-50 0.5827137 0.839 0.715 6.896152e-46
3012 12 6.104583e-21 0.5794064 0.868 0.778 1.469861e-16
2957 12 6.578284e-33 0.5774421 0.909 0.806 1.583919e-28
3057 12 8.209262e-15 0.5757581 0.970 0.940 1.976626e-10
2946 12 5.560978e-37 0.5751532 0.900 0.821 1.338972e-32
2966 12 1.202318e-31 0.5728397 0.899 0.833 2.894942e-27
2959 12 1.249564e-32 0.5655426 0.804 0.735 3.008701e-28
3054 12 4.224262e-15 0.5650529 0.953 0.916 1.017118e-10
3106 12 3.621689e-10 0.5613670 0.943 0.900 8.720304e-06
3086 12 1.225189e-11 0.5535442 0.962 0.924 2.950009e-07
2950 12 1.723374e-35 0.5520658 0.847 0.750 4.149540e-31
3001 12 1.970257e-23 0.5506943 0.891 0.807 4.743984e-19
2965 12 1.164753e-31 0.5481752 0.888 0.834 2.804492e-27
2954 12 1.769469e-33 0.5421068 0.809 0.709 4.260527e-29
2924 12 4.366474e-51 0.5385950 0.808 0.644 1.051360e-46
3107 12 3.970132e-10 0.5365269 0.959 0.936 9.559283e-06
2996 12 3.481665e-24 0.5346733 0.853 0.756 8.383154e-20
2970 12 2.937228e-30 0.5299717 0.901 0.812 7.072257e-26
3041 12 5.471120e-16 0.5294783 0.940 0.915 1.317336e-11
3009 12 3.056596e-21 0.5290174 0.888 0.825 7.359672e-17
3119 12 5.204180e-09 0.5243551 0.925 0.858 1.253062e-04
2956 12 5.908923e-33 0.5229395 0.769 0.638 1.422751e-28
2945 12 1.046275e-37 0.5226878 0.838 0.747 2.519220e-33
3078 12 4.454335e-13 0.5185085 0.932 0.888 1.072515e-08
2948 12 9.090296e-37 0.5177514 0.803 0.691 2.188762e-32
3064 12 3.494068e-14 0.5153472 0.860 0.754 8.413016e-10
3089 12 1.990313e-11 0.5138625 0.907 0.852 4.792276e-07
3076 12 3.569818e-13 0.5116079 0.851 0.766 8.595408e-09
2967 12 1.356907e-31 0.5089915 0.860 0.770 3.267161e-27
2990 12 2.845356e-26 0.5083540 0.840 0.736 6.851049e-22
3003 12 1.151055e-22 0.5067382 0.817 0.817 2.771509e-18
3137 12 2.320430e-07 0.5051090 0.801 0.782 5.587131e-03
3083 12 9.872859e-13 0.4971301 0.815 0.758 2.377187e-08
3025 12 3.425821e-19 0.4956660 0.868 0.806 8.248693e-15
3097 12 6.576947e-11 0.4906259 0.869 0.789 1.583597e-06
2921 12 8.227271e-56 0.4902571 0.723 0.543 1.980962e-51
3040 12 4.998221e-16 0.4886329 0.855 0.780 1.203472e-11
3085 12 3.289698e-12 0.4828577 0.337 0.219 7.920935e-08
2952 12 1.732671e-34 0.4794895 0.749 0.643 4.171925e-30
2961 12 3.930541e-32 0.4759427 0.795 0.670 9.463956e-28
3115 12 2.014664e-09 0.4739975 0.893 0.823 4.850908e-05
3127 12 1.190792e-07 0.4702633 0.876 0.843 2.867189e-03
2972 12 6.399843e-30 0.4702569 0.650 0.508 1.540954e-25
3080 12 6.363857e-13 0.4672990 0.802 0.729 1.532289e-08
3026 12 8.901131e-19 0.4662484 0.806 0.726 2.143214e-14
2975 12 2.511764e-29 0.4625293 0.764 0.640 6.047824e-25
3013 12 6.402276e-21 0.4585287 0.813 0.725 1.541540e-16
3015 12 9.616198e-21 0.4566583 0.631 0.787 2.315388e-16
2980 12 4.597765e-28 0.4558981 0.586 0.605 1.107050e-23
3067 12 5.506404e-14 0.4525914 0.851 0.784 1.325832e-09
3142 12 4.113136e-07 0.4522879 0.886 0.835 9.903609e-03
3030 12 1.226800e-17 0.4503268 0.838 0.779 2.953890e-13
2991 12 5.014838e-26 0.4454430 0.746 0.618 1.207473e-21
2955 12 3.384281e-33 0.4452460 0.721 0.603 8.148672e-29
2971 12 3.001871e-30 0.4400096 0.720 0.596 7.227905e-26
2984 12 3.711328e-27 0.4372834 0.680 0.523 8.936136e-23
2943 12 9.517114e-39 0.4366635 0.755 0.639 2.291531e-34
3143 12 6.261107e-07 0.4363626 0.802 0.753 1.507549e-02
3124 12 6.012528e-08 0.4342427 0.643 0.552 1.447696e-03
3091 12 2.605415e-11 0.4339156 0.615 0.520 6.273318e-07
2911 12 1.291957e-62 0.4296550 0.533 0.504 3.110775e-58
3135 12 2.081912e-07 0.4208607 0.837 0.807 5.012827e-03
3011 12 4.574101e-21 0.4181667 0.755 0.686 1.101352e-16
3090 12 2.291553e-11 0.4174120 0.761 0.657 5.517601e-07
2922 12 1.750445e-55 0.4171685 0.605 0.431 4.214720e-51
3139 12 2.693748e-07 0.4113883 0.997 0.996 6.486006e-03
3132 12 1.911078e-07 0.4039756 0.998 0.993 4.601495e-03
3072 12 1.542686e-13 0.4032524 0.802 0.756 3.714479e-09
3118 12 3.676596e-09 0.3956879 1.000 0.994 8.852507e-05
2974 12 7.193629e-30 0.3940197 0.592 0.543 1.732082e-25
3133 12 1.949636e-07 0.3895233 0.790 0.728 4.694333e-03
2949 12 3.902009e-36 0.3872250 0.608 0.478 9.395258e-32
3069 12 6.209156e-14 0.3850962 0.703 0.602 1.495041e-09
3079 12 5.681444e-13 0.3837040 0.759 0.684 1.367978e-08
3055 12 6.790083e-15 0.3831854 0.481 0.362 1.634916e-10
3071 12 1.250544e-13 0.3819645 0.735 0.671 3.011061e-09
3037 12 8.435689e-17 0.3818124 1.000 1.000 2.031145e-12
3123 12 4.245716e-08 0.3775322 0.762 0.684 1.022283e-03
3131 12 1.780438e-07 0.3717544 0.992 0.995 4.286938e-03
3096 12 5.165760e-11 0.3700255 0.994 0.985 1.243812e-06
3077 12 3.621110e-13 0.3698627 0.678 0.574 8.718908e-09
3008 12 1.052502e-21 0.3671490 1.000 1.000 2.534214e-17
3092 12 2.641142e-11 0.3658475 0.712 0.608 6.359341e-07
3084 12 2.192866e-12 0.3654555 0.694 0.677 5.279983e-08
3006 12 3.787971e-22 0.3635997 1.000 1.000 9.120677e-18
3033 12 2.172623e-17 0.3628883 0.999 0.998 5.231241e-13
3114 12 1.634618e-09 0.3587551 0.724 0.695 3.935833e-05
2985 12 8.699300e-27 0.3579215 0.627 0.497 2.094617e-22
2979 12 3.394588e-28 0.3575394 0.464 0.362 8.173490e-24
3024 12 3.229280e-19 0.3573475 0.999 0.999 7.775460e-15
3104 12 2.215647e-10 0.3553449 0.982 0.983 5.334834e-06
3126 12 9.296161e-08 0.3552499 0.766 0.746 2.238330e-03
3117 12 2.327743e-09 0.3539942 0.980 0.971 5.604739e-05
3140 12 3.806657e-07 0.3538464 0.971 0.972 9.165668e-03
3130 12 1.615931e-07 0.3531152 0.965 0.972 3.890838e-03
3113 12 1.262379e-09 0.3531063 0.986 0.990 3.039556e-05
3000 12 1.252620e-23 0.3528214 0.612 0.485 3.016058e-19
3149 12 1.867606e-06 0.3525789 0.990 0.995 4.496822e-02
3088 12 1.721967e-11 0.3522546 0.486 0.386 4.146151e-07
3100 12 1.192820e-10 0.3444284 0.662 0.576 2.872073e-06
3122 12 3.580272e-08 0.3441122 0.975 0.981 8.620579e-04
3038 12 8.625236e-17 0.3433945 0.589 0.452 2.076784e-12
3065 12 4.478936e-14 0.3431447 0.979 0.994 1.078438e-09
3035 12 3.061773e-17 0.3415697 0.637 0.555 7.372136e-13
3032 12 1.865841e-17 0.3413163 0.646 0.546 4.492573e-13
3128 12 1.304268e-07 0.3374239 0.670 0.582 3.140417e-03
3075 12 2.220511e-13 0.3364133 0.625 0.535 5.346547e-09
2944 12 1.254186e-38 0.3356295 0.496 0.468 3.019828e-34
3016 12 1.867559e-20 0.3324909 0.998 0.998 4.496709e-16
3014 12 7.312598e-21 0.3319052 0.587 0.473 1.760727e-16
3111 12 8.229942e-10 0.3278067 0.942 0.971 1.981605e-05
3098 12 8.833803e-11 0.3268954 0.671 0.602 2.127003e-06
3053 12 3.568580e-15 0.3268396 0.980 0.980 8.592426e-11
3045 12 1.172597e-15 0.3264920 0.965 0.966 2.823378e-11
3136 12 2.249982e-07 0.3259449 0.626 0.677 5.417507e-03
3034 12 2.408529e-17 0.3258396 0.609 0.504 5.799257e-13
3108 12 5.301461e-10 0.3251004 0.968 0.962 1.276486e-05
3010 12 4.356853e-21 0.3244262 0.992 0.995 1.049043e-16
3145 12 7.876434e-07 0.3243332 0.867 0.860 1.896488e-02
3029 12 6.321913e-18 0.3231173 0.989 0.992 1.522190e-13
2931 12 2.213391e-48 0.3228607 0.505 0.375 5.329403e-44
3002 12 1.121855e-22 0.3218900 0.996 0.997 2.701201e-18
3125 12 7.784361e-08 0.3206946 0.628 0.535 1.874318e-03
3005 12 1.654523e-22 0.3178707 0.999 0.998 3.983759e-18
2964 12 8.161483e-32 0.3170956 1.000 1.000 1.965122e-27
3101 12 1.291977e-10 0.3154902 0.580 0.494 3.110823e-06
3066 12 4.737148e-14 0.3136689 0.584 0.486 1.140611e-09
3048 12 1.519755e-15 0.3122709 0.984 0.988 3.659266e-11
3120 12 2.338021e-08 0.3116574 0.922 0.933 5.629487e-04
2963 12 5.345145e-32 0.3076487 1.000 0.999 1.287004e-27
2989 12 2.140523e-26 0.3059965 0.998 0.996 5.153951e-22
3074 12 2.081265e-13 0.3039921 0.945 0.953 5.011269e-09
2998 12 6.267290e-24 0.3035860 0.992 0.995 1.509038e-19
3007 12 5.616278e-22 0.3035051 0.998 0.998 1.352287e-17
2987 12 1.869819e-26 0.3030256 1.000 1.000 4.502151e-22
3004 12 1.389846e-22 0.3025490 0.553 0.446 3.346470e-18
2927 12 2.924437e-50 0.3022764 0.407 0.325 7.041460e-46
2993 12 2.192097e-25 0.3021086 0.994 0.988 5.278130e-21
3020 12 3.513109e-20 0.2968731 0.979 0.987 8.458864e-16
3056 12 6.860246e-15 0.2954164 0.875 0.906 1.651810e-10
3021 12 8.708380e-20 0.2923405 0.543 0.431 2.096804e-15
3094 12 3.006929e-11 0.2914263 0.910 0.910 7.240084e-07
3049 12 1.700830e-15 0.2911914 0.955 0.959 4.095259e-11
3105 12 3.068921e-10 0.2903090 0.912 0.936 7.389349e-06
3047 12 1.498777e-15 0.2881936 0.942 0.927 3.608754e-11
3052 12 2.733483e-15 0.2866858 0.954 0.966 6.581680e-11
3110 12 8.216157e-10 0.2862649 0.565 0.496 1.978286e-05
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2165 12 1.018225e-305 -0.6134389 0.238 0.773 2.451682e-301
2079 12 0.000000e+00 -0.6164725 0.853 1.000 0.000000e+00
2080 12 0.000000e+00 -0.6180724 0.400 0.884 0.000000e+00
2251 12 4.798737e-238 -0.6184027 0.622 0.902 1.155440e-233
2081 12 0.000000e+00 -0.6186290 0.555 0.940 0.000000e+00
2082 12 0.000000e+00 -0.6231384 0.326 0.880 0.000000e+00
2169 12 7.594470e-299 -0.6237574 0.168 0.760 1.828596e-294
2390 12 2.435324e-189 -0.6246703 0.060 0.551 5.863774e-185
2488 12 5.770768e-164 -0.6286257 0.041 0.626 1.389486e-159
2083 12 0.000000e+00 -0.6292587 0.260 0.815 0.000000e+00
2219 12 2.531172e-267 -0.6312435 0.117 0.784 6.094555e-263
2175 12 9.588183e-293 -0.6359800 0.212 0.746 2.308643e-288
2270 12 4.644787e-230 -0.6403940 0.092 0.683 1.118372e-225
2084 12 0.000000e+00 -0.6404564 0.198 0.809 0.000000e+00
2085 12 0.000000e+00 -0.6421550 0.669 0.992 0.000000e+00
2395 12 1.265895e-188 -0.6435194 0.047 0.647 3.048022e-184
2180 12 1.261491e-289 -0.6436512 0.176 0.746 3.037418e-285
2086 12 0.000000e+00 -0.6450464 0.827 0.999 0.000000e+00
2087 12 0.000000e+00 -0.6477677 0.771 0.979 0.000000e+00
2231 12 1.519055e-254 -0.6501797 0.601 0.924 3.657580e-250
2088 12 0.000000e+00 -0.6512030 0.249 0.822 0.000000e+00
2248 12 7.814237e-241 -0.6565571 0.108 0.674 1.881512e-236
2173 12 2.601412e-295 -0.6575380 0.297 0.772 6.263680e-291
2200 12 1.103356e-277 -0.6607071 0.128 0.772 2.656661e-273
2430 12 1.716208e-178 -0.6632414 0.035 0.559 4.132286e-174
2305 12 1.909946e-214 -0.6663756 0.130 0.559 4.598767e-210
2217 12 8.348527e-269 -0.6685944 0.120 0.799 2.010158e-264
2089 12 0.000000e+00 -0.6700642 0.335 0.899 0.000000e+00
2090 12 0.000000e+00 -0.6731121 0.354 0.850 0.000000e+00
2211 12 2.751543e-271 -0.6733764 0.115 0.810 6.625165e-267
2226 12 1.995339e-259 -0.6780798 0.399 0.779 4.804377e-255
2091 12 0.000000e+00 -0.6792095 0.750 0.975 0.000000e+00
2092 12 0.000000e+00 -0.6795942 0.171 0.843 0.000000e+00
2093 12 0.000000e+00 -0.6827244 0.865 1.000 0.000000e+00
2176 12 1.232868e-292 -0.6837251 0.118 0.800 2.968499e-288
2259 12 1.604078e-234 -0.6850852 0.072 0.798 3.862300e-230
2184 12 1.731055e-287 -0.6854173 0.129 0.812 4.168034e-283
2094 12 0.000000e+00 -0.6855268 0.386 0.917 0.000000e+00
2341 12 4.480356e-203 -0.6855900 0.046 0.645 1.078780e-198
2095 12 0.000000e+00 -0.6865198 0.730 0.995 0.000000e+00
2096 12 0.000000e+00 -0.6934495 0.246 0.868 0.000000e+00
2194 12 1.357946e-281 -0.6936349 0.124 0.817 3.269662e-277
2097 12 0.000000e+00 -0.6941179 0.317 0.905 0.000000e+00
2192 12 3.782550e-282 -0.6967576 0.111 0.795 9.107625e-278
2238 12 3.546340e-251 -0.6979157 0.348 0.734 8.538877e-247
2098 12 0.000000e+00 -0.6996461 0.183 0.763 0.000000e+00
2099 12 0.000000e+00 -0.7005891 0.421 0.935 0.000000e+00
2100 12 0.000000e+00 -0.7042925 0.354 0.867 0.000000e+00
2245 12 1.528740e-243 -0.7063975 0.419 0.804 3.680899e-239
2101 12 0.000000e+00 -0.7072108 0.835 0.999 0.000000e+00
2189 12 2.830588e-283 -0.7073061 0.116 0.795 6.815491e-279
2102 12 0.000000e+00 -0.7097213 0.558 0.979 0.000000e+00
2167 12 1.425591e-301 -0.7146120 0.234 0.724 3.432539e-297
2378 12 8.556079e-193 -0.7199610 0.045 0.747 2.060133e-188
2103 12 0.000000e+00 -0.7233920 0.212 0.842 0.000000e+00
2260 12 1.981316e-234 -0.7239916 0.074 0.793 4.770613e-230
2104 12 0.000000e+00 -0.7253784 0.371 0.916 0.000000e+00
2343 12 8.256766e-203 -0.7253824 0.543 0.840 1.988064e-198
2387 12 1.216527e-190 -0.7311709 0.039 0.807 2.929154e-186
2216 12 1.889672e-269 -0.7313916 0.434 0.847 4.549952e-265
2105 12 0.000000e+00 -0.7381918 0.236 0.887 0.000000e+00
2106 12 0.000000e+00 -0.7409302 0.131 0.788 0.000000e+00
2107 12 0.000000e+00 -0.7448708 0.365 0.861 0.000000e+00
2108 12 0.000000e+00 -0.7464335 0.909 1.000 0.000000e+00
2199 12 5.785917e-278 -0.7576467 0.090 0.828 1.393133e-273
2109 12 0.000000e+00 -0.7599929 0.243 0.847 0.000000e+00
2170 12 1.073760e-298 -0.7655769 0.146 0.695 2.585400e-294
2110 12 0.000000e+00 -0.7709099 0.158 0.857 0.000000e+00
2111 12 0.000000e+00 -0.7715693 0.169 0.844 0.000000e+00
2112 12 0.000000e+00 -0.7756508 0.133 0.793 0.000000e+00
2113 12 0.000000e+00 -0.7895862 0.400 0.791 0.000000e+00
2307 12 3.886550e-214 -0.7941424 0.090 0.540 9.358036e-210
2114 12 0.000000e+00 -0.7961270 0.449 0.882 0.000000e+00
2201 12 2.813645e-277 -0.8088716 0.097 0.825 6.774694e-273
2115 12 0.000000e+00 -0.8108053 0.130 0.741 0.000000e+00
2116 12 0.000000e+00 -0.8201162 0.157 0.797 0.000000e+00
2164 12 2.483470e-307 -0.8353496 0.094 0.843 5.979699e-303
2117 12 0.000000e+00 -0.8369631 0.242 0.888 0.000000e+00
2205 12 2.743689e-274 -0.8435958 0.169 0.607 6.606256e-270
2118 12 0.000000e+00 -0.8440326 0.335 0.780 0.000000e+00
2225 12 3.833156e-260 -0.8543148 0.160 0.545 9.229474e-256
2119 12 0.000000e+00 -0.8564741 0.640 0.972 0.000000e+00
2120 12 0.000000e+00 -0.8601576 0.552 0.971 0.000000e+00
2121 12 0.000000e+00 -0.8638207 0.629 0.982 0.000000e+00
2122 12 0.000000e+00 -0.8717619 0.551 0.795 0.000000e+00
2123 12 0.000000e+00 -0.8763949 0.817 0.949 0.000000e+00
2124 12 0.000000e+00 -0.8781101 0.566 0.984 0.000000e+00
2125 12 0.000000e+00 -0.8835162 0.582 0.977 0.000000e+00
2126 12 0.000000e+00 -0.8874138 0.382 0.940 0.000000e+00
2227 12 7.553348e-259 -0.8972211 0.064 0.648 1.818695e-254
2127 12 0.000000e+00 -0.9037984 0.327 0.908 0.000000e+00
2128 12 0.000000e+00 -0.9063511 0.188 0.881 0.000000e+00
2129 12 0.000000e+00 -0.9112763 0.562 0.986 0.000000e+00
2130 12 0.000000e+00 -0.9219611 0.381 0.966 0.000000e+00
2131 12 0.000000e+00 -0.9373251 0.090 0.784 0.000000e+00
2132 12 0.000000e+00 -0.9451443 0.442 0.930 0.000000e+00
2133 12 0.000000e+00 -0.9493460 0.752 0.917 0.000000e+00
2134 12 0.000000e+00 -0.9545360 0.092 0.854 0.000000e+00
2135 12 0.000000e+00 -0.9604329 0.262 0.884 0.000000e+00
2136 12 0.000000e+00 -0.9622743 0.192 0.849 0.000000e+00
2137 12 0.000000e+00 -0.9730315 0.369 0.968 0.000000e+00
2138 12 0.000000e+00 -0.9846268 0.724 0.998 0.000000e+00
2139 12 0.000000e+00 -1.0100344 0.243 0.946 0.000000e+00
2140 12 0.000000e+00 -1.0165932 0.156 0.891 0.000000e+00
2171 12 1.514850e-297 -1.0180213 0.061 0.872 3.647456e-293
2141 12 0.000000e+00 -1.0238471 0.116 0.884 0.000000e+00
2142 12 0.000000e+00 -1.0402266 0.181 0.587 0.000000e+00
2143 12 0.000000e+00 -1.0543828 0.758 0.999 0.000000e+00
2144 12 0.000000e+00 -1.0591907 0.144 0.904 0.000000e+00
2145 12 0.000000e+00 -1.0760617 0.287 0.952 0.000000e+00
2146 12 0.000000e+00 -1.1051841 0.429 0.974 0.000000e+00
2147 12 0.000000e+00 -1.1182616 0.197 0.751 0.000000e+00
2148 12 0.000000e+00 -1.1423616 0.311 0.969 0.000000e+00
2149 12 0.000000e+00 -1.2330423 0.129 0.679 0.000000e+00
2150 12 0.000000e+00 -1.2420304 0.259 0.813 0.000000e+00
2151 12 0.000000e+00 -1.2653708 0.335 0.865 0.000000e+00
2152 12 0.000000e+00 -1.2847646 0.322 0.921 0.000000e+00
2153 12 0.000000e+00 -1.4034415 0.174 0.964 0.000000e+00
2154 12 0.000000e+00 -1.4308999 0.270 0.865 0.000000e+00
2155 12 0.000000e+00 -1.5794227 0.527 0.996 0.000000e+00
2156 12 0.000000e+00 -1.6314050 0.207 0.963 0.000000e+00
2157 12 0.000000e+00 -1.7091193 0.203 0.953 0.000000e+00
2158 12 0.000000e+00 -1.8664315 0.304 0.944 0.000000e+00
2159 12 0.000000e+00 -2.1738990 0.571 0.999 0.000000e+00
2160 12 0.000000e+00 -2.1803482 0.617 0.998 0.000000e+00
2161 12 0.000000e+00 -2.4003554 0.154 0.992 0.000000e+00
2162 12 0.000000e+00 -2.4984584 0.573 1.000 0.000000e+00
2163 12 0.000000e+00 -3.4917593 0.955 1.000 0.000000e+00
gene
2049 RAB13
2255 ACTB
2846 TPM2
2608 ANXA2
2625 LDHA
2812 PRDX1
2919 CCND1
2813 MYL12B
2598 MAP1B
2910 MYL12A
2753 SKP1
2912 ANXA1
2202 DYNC1LI2
2891 NQO1
2892 LDHB
2942 TPM1
2633 SNRPD2
2977 CRYAB
2941 ACTG1
2893 PPIA
2904 ANXA5
2807 PGK1
2804 ATP5B
2937 NPM1
2999 KRT7
3138 TAGLN
2994 S100A11
2934 PKM
2867 VDAC1
2958 GAPDH
2915 ARF4
3116 MYL9
2983 EIF4A1
2962 ALDOA
2933 TALDO1
2976 ENO1
2951 ARPC3
2917 ANP32B
2938 GSTO1
3059 VIM
2940 RHOA
3051 S100A6
3058 UCHL1
3019 COTL1
2916 MAP4
2918 PALLD
2960 CSRP1
3028 SEPT7
2973 ATP5H
2995 PRDX6
3148 UBB
2968 PSMB3
3134 GSTP1
3129 RPS27L
3018 MGST3
3070 UQCRB
3044 HSPB1
2978 YWHAQ
2900 MDH1
3039 ATP5J2
2935 TCEAL4
2932 CCT8
2986 PSMD2
2997 HNRNPA3
3103 TPI1
2992 EIF3I
3112 LINC01133
3036 CDC42
3073 CYCS
2988 KIF5B
3046 FKBP1A
2936 GLRX3
3087 NME1
2926 CHMP5
3012 CCT5
2957 COPS6
3057 VDAC2
2946 SDHC
2966 GHITM
2959 HNRNPH3
3054 CAPZB
3106 CLTA
3086 C14orf166
2950 XRCC6
3001 ATP5F1
2965 ARPC4
2954 CCT7
2924 PSMC1
3107 SMS
2996 ESD
2970 NDUFB6
3041 PGAM1
3009 MDH2
3119 PSMA4
2956 ANXA6
2945 GLO1
3078 ATP5C1
2948 SDCBP
3064 PSME2
3089 PSMA1
3076 MAP1LC3B
2967 SCP2
2990 CMPK1
3003 CORO1C
3137 TUBA1A
3083 MIF
3025 PRDX3
3097 PSMB2
2921 PPP1R7
3040 CAPZA2
3085 NEFM
2952 MOCS2
2961 COPS8
3115 RNF181
3127 CAPN2
2972 PRPS1
3080 ANXA7
3026 PSMC3
2975 VBP1
3013 VAMP3
3015 UACA
2980 ZEB1
3067 ECHS1
3142 UBE2N
3030 SNRPC
2991 ARL1
2955 PSME1
2971 UQCRC2
2984 PSMC4
2943 ETFA
3143 CCT2
3124 TYMS
3091 SLC9A3R2
2911 KIF1C
3135 GDI2
3011 ATP6V1E1
3090 PRMT1
2922 ANXA4
3139 COX7C
3132 COX4I1
3072 ADI1
3118 PFDN5
2974 HTATSF1
3133 PSMD4
2949 ACOT7
3069 UCHL3
3079 MCTS1
3055 HIST1H2BK
3071 PARVA
3037 RPL31
3123 RSU1
3131 PSMA7
3096 COX5B
3077 PSMD13
3008 TMSB4X
3092 POLR2G
3084 PPP2R1A
3006 RPL35
3033 BTF3
3114 HNRNPM
2985 HADHB
2979 PSMC3IP
3024 NACA
3104 SHFM1
3126 SDHB
3117 PRDX5
3140 ATPIF1
3130 HSBP1
3113 SUB1
3000 HPRT1
3149 PABPC1
3088 CKB
3100 CETN2
3122 RBX1
3038 FH
3065 HMGB1
3035 RALB
3032 PPA2
3128 ADK
3075 CYB5B
2944 PINK1
3016 CHCHD2
3014 IDH3G
3111 NCL
3098 NDUFA10
3053 DBI
3045 NDUFA11
3136 PTPN11
3034 DECR1
3108 PEBP1
3010 UBL5
3145 STMN1
3029 NDUFB2
2931 TSR2
3002 ATP5L
3125 ACTR10
3005 COX7A2
2964 FAU
3101 CAPG
3066 ACAT1
3048 ATP5G3
3120 PFDN2
2963 HINT1
2989 UQCRH
3074 LSM3
2998 CSTB
3007 UQCRQ
2987 TMSB10
3004 BCCIP
2927 TRAK2
2993 EDF1
3020 BRK1
3056 UBC
3021 COPS4
3094 DDT
3049 TXNDC17
3105 MRFAP1
3047 EIF3E
3052 COX7A2L
3110 OSTF1
3050 C12orf75
3061 C4orf3
3068 TMEM14C
3093 NDUFB11
3146 NAA10
3042 ARF1
2969 TCEB2
3023 ATOX1
3099 HARS
3043 CUTA
2982 RPS26
3081 CALM3
3017 S100A13
2953 COX8A
3147 PEPD
2925 RPL22
3063 PTGES3
3141 UBE2V2
3082 TRAPPC1
3060 TAX1BP3
3027 HNRNPC
3109 ATP5D
2981 MINOS1
3102 CCT3
3095 FIS1
3144 THOC7
2939 RPL38
3022 SLIRP
3031 MPC2
3062 PDAP1
2947 CALM2
3121 MVP
2837 CDC25B
2697 CDC42BPB
2749 PURA
2825 MFAP2
2802 HHIP-AS1
2854 PKD2
2928 FOSB
2853 TFRC
2842 BIRC6
2514 CBX5
2422 JAK1
2897 PIK3R1
2778 NCBP2-AS2
2838 MIA3
2507 DDX18
2826 DHRS3
2782 PLOD3
2593 ADD3
2781 COLGALT1
2886 FBXO5
2691 SLC25A37
2661 IFNGR2
2848 KIF20B
2905 SCRG1
2679 CERCAM
2730 WAPAL
2693 PBRM1
2466 TMOD3
2571 APH1A
2708 MBD4
2876 AHR
2828 SLC8A1
2923 RDH10
2880 ATP10D
2874 TM2D3
2676 YTHDC1
2750 PPP3CA
2702 NFIA
2462 LSM10
2801 PRKCA
2704 PGP
2453 ERGIC3
2618 MAP2K3
2818 SAV1
2638 DIAPH3
2712 SMC5
2877 ARHGEF2
2644 DESI2
2834 SAMD11
2894 PUM1
2642 SEC14L1
2539 CCDC59
2578 CLINT1
2715 EGLN2
2304 SEC62
2486 HEBP2
2597 C11orf24
2371 RALBP1
2621 PTEN
2784 CALHM2
2732 SMPD1
2914 MAGI1
2717 LINC00667
2396 ZYX
2908 HIST1H1A
2883 RNF19A
2823 VPS13A
2742 EPB41L4A-AS1
2788 ATAD2
2374 MRPS12
2652 UBE2J2
2747 MYH10
2759 HERC2
2896 PGF
2612 C6orf62
2887 EMILIN2
2677 TMEM30A
2709 CCDC47
2868 FILIP1L
2808 FNBP4
2727 SMCHD1
2711 SAT1
2865 ARL4D
2705 FKBP9
2859 PLAT
2792 AKAP12
2699 SLC39A6
2545 KATNBL1
2771 PHIP
2491 HDGF
2907 PDGFRB
2639 TSSC4
2824 KDM5A
2658 GPC1
2651 KCMF1
2775 ADAR
2657 CTSA
2670 MANF
2762 HOXC8
2899 ARID1A
2890 NFKBIA
2744 VPS4B
2879 HIST2H2AC
2920 ZNF292
2576 PHLDA3
2665 FAM133B
2232 CD63
2819 ACSL3
2856 ZKSCAN1
2528 SORBS3
2646 TEX264
2538 ACLY
2650 AGPAT2
2888 MAFG
2706 PHF14
2649 GCC2
2489 FLYWCH2
2321 NAA38
2864 AAK1
2873 RGMB
2554 PJA2
2689 TLK1
2688 TMEM203
2448 LRRFIP1
2869 COL16A1
2852 HMMR
2909 ZFHX3
2754 KPNA6
2752 MGAT2
2796 TMEM259
2800 SETX
2790 LEPREL4
2849 KIAA0947
2722 EIF4G3
2605 VGLL3
2692 TMEM243
2855 ZBTB7A
2898 TNRC6A
2766 PCYOX1
2743 PLEKHO1
2615 SETD5-AS1
2476 PLEKHJ1
2543 LRPAP1
2610 SRSF4
2858 KLF2
2884 MEIS2
2634 TM2D2
2562 CD320
2405 GNB1
2233 SSR3
2567 UBE3A
2930 UNC5B
2542 AMD1
2805 TRIO
2629 CSNK1G3
2569 SS18L2
2817 ECE1
2635 CHPF
2524 C12orf44
2716 ATP1A1
2793 METRNL
2696 SLC52A2
2580 RAB31
2821 SLC7A1
2582 AHCYL1
2913 HOXA5
2404 MYO1C
2678 PTPN12
2401 DDX24
2803 ERRFI1
2799 TUSC1
2559 SCARB2
2572 KRAS
2723 KAZALD1
2663 CBX6
2731 NXT1
2798 ABI3BP
2795 NIN
2515 CGGBP1
2190 B2M
2666 MARCH7
2685 GNAQ
2721 RRP36
2468 SURF4
2694 C1GALT1
2613 P4HA2
2536 APPL1
2359 UBXN4
2686 BAZ1A
2789 DBF4
2484 DDX3X
2622 CTSZ
2681 TP53I11
2603 SEPHS2
2337 DNAJC19
2636 FAM63B
2687 TGFBR2
2850 IRF2BP2
2767 TES
2902 G0S2
2586 MPZL1
2748 ARHGAP21
2680 RNMT
2495 RAD50
2606 TRIP12
2669 SMAD5
2906 VEGFA
2713 CSNK1E
2857 LBR
2616 PHF3
2783 TMEM87A
2627 CHD2
2289 FHL2
2520 CHD4
2517 HNRNPUL1
2822 CEP55
2315 SSNA1
2475 MAP2K2
2881 POLR2J3
2718 TAOK1
2797 SGOL2
2844 ATP1B1
2377 SFT2D1
2684 CCDC12
2786 FRMD4A
2791 REV3L
2592 CCDC107
2872 PTPRF
2736 SACS
2734 FADS3
2830 CENPE
2556 SSBP4
2585 FLNA
2809 RBM26
2473 COPA
2720 PAM
2889 ABL2
2604 ELOVL1
2833 SLC7A5
2773 BMPR2
2839 CENPA
2455 GADD45A
2334 ACTN4
2645 NRBF2
2840 ZFC3H1
2811 PRRC2A
2794 CDC42EP2
2595 TAOK3
2619 HOXB2
2594 HERC4
2460 BCL7C
2516 MIER1
2532 PARP1
2587 ANKIB1
2568 SYNE1
2319 ERP29
2758 ANPEP
2614 MARK3
2623 SENP6
2829 MYC
2445 C19orf10
2498 BDP1
2570 MPHOSPH8
2480 FNDC3B
2547 IMP3
2726 CREB3L2
2632 SVIL
2660 TSC22D4
2458 PSMG3
2333 TSPAN4
2523 RB1CC1
2719 ADAM10
2863 VEPH1
2521 RPN1
2841 AURKA
2478 SMIM12
2738 TRIB3
2415 PLIN2
2737 SEMA7A
2574 PABPN1
2279 SPATS2L
2656 SH3RF1
2698 CHD1
2785 ATP2A2
2557 TBL1XR1
2540 PCOLCE
2733 TENM3
2440 DNAJC10
2418 SRSF7
2860 NOTCH2
2438 FAM120A
2655 SRGN
2628 NABP1
2836 MRC2
2831 POLR2A
2607 METRN
2671 ZNF22
2662 H2AFX
2768 CLSTN1
2779 PEAK1
2314 VAT1
2861 EGFR
2428 RBFOX2
2456 CCM2
2555 DNAJC1
2350 ZDHHC12
2847 NUFIP2
2810 JMJD1C
2325 ARL6IP5
2502 BRD7
2637 ANKLE2
2206 RTN4
2725 HELLS
2845 TCF7L2
2772 RNF24
2347 GOLGA4
2513 CEBPG
2511 PPP2CB
2741 ATOH8
2348 MYOF
2467 DNMT1
2323 CNPY2
2673 DDIT3
2534 SLC39A7
2851 EPC1
2399 MESDC2
2577 ITGB5
2903 FAM43A
2815 LY6K
2566 ASH1L
2526 SNHG7
2474 SPATS2
2866 ANKRD1
2664 HHIP
2871 ZNF503
2509 LINC00657
2330 ENAH
2882 RBBP6
2724 CDK12
2373 LSM6
2522 CHIC2
2564 MYCBP2
2302 NEXN
2653 TSPAN5
2561 CTBP1
2827 ZNF281
2454 RSF1
2471 RALGPS2
2787 PIEZO1
2640 ATXN2
2299 TAF1D
2461 AFAP1
2298 JTB
2757 KLF3
2583 GGNBP2
2620 CDH13
2630 USP22
2654 HOOK3
2728 UBN1
2485 UBE2M
2439 UBE2R2
2527 SLFN5
2533 PLAUR
2510 PRKAR2A
2776 SEMA3C
2672 AFF4
2591 ABHD17A
2414 ASCC3
2581 SEC24D
2602 MMP14
2426 RSRC2
2410 SPCS3
2413 PPIG
2609 DSEL
2470 PPP4R2
2589 PTPN14
2751 TSC22D1
2575 CCDC88A
2465 MAP7D1
2501 MFGE8
2329 YWHAG
2477 HTRA1
2531 HLA-B
2641 TM9SF2
2535 MAP7D3
2590 MCL1
2674 NIPBL
2384 NNMT
2806 SETD5
2596 GOPC
2668 CKAP2
2345 ZNF106
2494 APP
2332 DST
2464 CRELD2
2769 IL6
2496 PXDC1
2518 SKIL
2770 AMOTL2
2411 RPN2
2419 RFC1
2435 USP34
2675 TACC1
2774 PLAGL1
2346 SHC1
2763 LUM
2351 IKBIP
2835 KMT2A
2552 NCOA7
2901 SLC7A11
2370 HNRNPAB
2600 SLC4A7
2469 SDF2
2765 FYN
2424 RBM27
2870 HIST1H1B
2322 SSR1
2451 CTSL
2354 GLIPR1
2683 NTN4
2394 C5orf24
2437 HECTD1
2253 TPR
2862 ADAMTS6
2367 CLIP1
2695 GTSE1
2599 RNF213
2436 CHTOP
2626 EML4
2746 SCN9A
2441 GRN
2483 ASAP2
2735 MKNK2
2497 CHD9
2714 KLF4
2560 RBMS3
2643 NRP1
2388 PAWR
2369 CLMP
2756 FGF7
2294 PHACTR2
2579 RNF145
2703 RIF1
2739 JADE1
2271 LUC7L3
2408 VMP1
2832 CEP350
2425 DHX36
2291 DEK
2311 U2SURP
2284 YY1
2487 PLOD2
2503 JAGN1
2353 STAT1
2340 SDF4
2220 DDX5
2452 SNAI2
2363 TRA2B
2546 TMPO
2878 PI16
2386 GLS
2229 TRAM1
2537 ZNF148
2764 SEL1L
2647 ARID4B
2504 USP9X
2443 C19orf48
2701 SLC20A1
2357 IFI16
2659 LTBP1
2549 FOSL1
2506 CTBP2
2550 WAC
2558 NSD1
2700 SERTAD2
2393 HLA-C
2306 RTF1
2336 SHOC2
2400 PLEC
2293 HNRNPA0
2530 TGIF1
2573 HMGXB4
2710 PKN2
2463 TRIP11
2544 MIS18BP1
2379 MACF1
2631 VEGFC
2493 LUZP1
2406 ROCK2
2500 PNRC1
2588 SUZ12
2309 MYO1B
2308 EIF2AK4
2432 FGF2
2551 CDKN1A
2780 TNRC6B
2814 C1orf63
2366 KRCC1
2228 SRSF11
2479 RHOB
2364 HLA-A
2320 DPYSL2
2412 FGFR1
2342 GOLGB1
2215 CANX
2283 SEC63
2447 PLOD1
2417 CTDSP2
2611 ARHGAP35
2481 ANKRD12
2397 ELL2
2356 LARP1
2204 LY6E
2490 GADD45B
2331 PCM1
2288 MLEC
2365 CCDC85B
2328 FKBP10
2214 BSG
2193 SRRM1
2565 PMP22
2729 ZFP36
2177 PCBP1
2885 MIDN
2050 SIVA1
2446 NFIB
2247 RNPS1
2361 TOR1AIP2
2816 UGCG
2682 BDNF
2624 ITGAV
2273 LRP10
2261 BBX
2423 ZFAND5
2349 CREB3L1
2187 ZNF706
2051 MT-ND5
2300 ASAP1
2280 ADAM9
2296 PNN
2344 SH2D4A
2382 TAF10
2402 DNAJC3
2256 POP7
2667 WSB1
2191 IGFBP4
2601 SLC38A1
2335 QSOX1
2617 F3
2352 ATF5
2820 ACAN
2376 GALNT1
2272 MBNL1
2492 ITGA5
2429 RND3
2183 KPNB1
2276 ASPH
2252 HNRNPD
2433 MAT2A
2281 PGRMC2
2239 LMO7
2052 MRPL14
2541 ANKRD28
2381 SLC3A2
2740 SQLE
2269 BASP1
2210 HP1BP3
2777 HSPG2
2760 HIST1H1E
2258 SMC3
2403 ARHGAP29
2431 F2R
2745 FAT1
2053 HIF1A
2054 CD99
2287 CDC42EP1
2360 GPBP1
2237 CLTC
2209 WASF2
2420 KMT2E
2519 NKTR
2244 RRAS
2277 RAD21
2529 PODXL
2648 GLG1
2318 RBMS1
2310 WHSC1L1
2166 CD44
2755 TM4SF1
2358 MGAT1
2172 FOXP1
2472 ATP13A3
2355 ADAM12
2327 ARF6
2223 BCLAF1
2434 TCF4
2499 DDIT4
2207 FERMT2
2427 EEA1
2179 CTSB
2222 SCAF11
2391 BRD4
2055 NFIC
2875 HES1
2056 SPARC
2236 MMP2
2234 PPP1R12A
2303 DLC1
2292 XPO1
2457 ATP2B4
2313 PPP1R15A
2213 THY1
2257 BGN
2185 THRAP3
2326 MYADM
2761 CENPF
2389 SLC1A5
2442 CTSC
2843 ZFHX4
2278 TEAD1
2450 CDH11
2301 BPTF
2263 TM9SF3
2459 B4GALT1
2266 P4HA1
2895 KCNQ1OT1
2218 EIF4G1
2203 MICAL2
2421 SRGAP1
2264 PDIA4
2548 ANKRD37
2250 SMURF2
2057 GNAI2
2235 CD81
2282 KCTD20
2212 SRSF5
2690 PAPPA
2290 LPP
2254 IGFBP6
2265 MBNL2
2380 BRD2
2286 NFE2L2
2058 PDIA6
2249 TAF7
2339 RP11-572C15.6
2198 PAFAH1B1
2512 OXTR
2449 ARL6IP1
2407 TPX2
2221 GTF2I
2240 CEP170
2188 NCOR1
2707 EGR1
2285 SDF2L1
2275 ZBTB38
2182 PRSS23
2059 MYH9
2416 EFEMP1
2241 FRMD6
2525 TRAM2
2060 SSR2
2246 IL6ST
2224 DDX17
2508 AEBP1
2563 CCNL1
2409 VASN
2061 MT-CO1
2062 PDIA3
2553 TPBG
2268 USP1
2317 PHLDA1
2242 DCBLD2
2929 IGFBP5
2063 EIF5
2243 TGOLN2
2064 LOXL1
2065 MT-ND2
2372 NGF
2066 EPS8
2067 PRRX1
2324 H1FX
2262 SLC16A3
2196 SEC61A1
2392 TNFRSF1A
2274 NR3C1
2178 PSAP
2312 LTBP2
2338 SULF1
2584 THBS2
2362 JUN
2174 TJP1
2297 GANAB
2505 COL12A1
2375 RGS4
2068 ERLEC1
2069 OSBPL8
2197 N4BP2L2
2168 NT5E
2482 ZFP36L2
2230 CTDNEP1
2267 NAV1
2070 CDV3
2208 ARGLU1
2368 ZFP36L1
2071 KRT10
2186 BTG1
2398 CEBPD
2181 TMEM165
2316 FGF5
2072 TLN1
2383 JUNB
2073 TIMP2
2295 XBP1
2195 ATP2B1
2074 P4HB
2075 BRI3
2076 TMED9
2444 ASPM
2385 TOP2A
2077 CCDC80
2078 MT-ND1
2165 CEBPB
2079 MT-ND4
2080 MXRA8
2251 SERPINE1
2081 ATF4
2082 LMAN1
2169 CDC42EP3
2390 ELN
2488 HEG1
2083 GOLIM4
2219 VCL
2175 EVA1B
2270 IER2
2084 SPOCK1
2085 CALU
2395 PPAP2B
2180 ISLR
2086 MT-CYB
2087 IGFBP7
2231 TIMP3
2088 ALCAM
2248 FBLN2
2173 INHBA
2200 HERPUD1
2430 FOS
2305 TNFRSF11B
2217 CXXC5
2089 PRRC2C
2090 LMO4
2211 PNISR
2226 DCN
2091 TGFBI
2092 LOXL2
2093 MT-CO3
2176 LAMC1
2259 PXDN
2184 SPAG9
2094 ENG
2341 ADM
2095 CALR
2096 PRKDC
2194 EXT1
2097 VIMP
2192 CD248
2238 CYP1B1
2098 CITED2
2099 RBM39
2100 RHOBTB3
2245 CKS2
2101 MT-ATP6
2189 COL5A1
2102 FSTL1
2167 CRLF1
2378 PDGFRA
2103 CDH2
2260 AKAP9
2104 APLP2
2343 IGFBP3
2387 XIST
2216 SERPINE2
2105 SON
2106 COL4A2
2107 COL6A2
2108 MT-CO2
2199 LRP1
2109 PRRX2
2170 PTGIS
2110 EMP1
2111 CRIM1
2112 DUSP1
2113 GREM1
2307 HAS2
2114 CLDN11
2201 NR2F2
2115 COL4A1
2116 IER3
2164 COL5A2
2117 SRRM2
2205 FST
2118 HMGB2
2225 MKI67
2119 TXNRD1
2120 LOX
2121 LIMA1
2122 UBE2S
2123 PPP1R14B
2124 AHNAK
2125 MARCKS
2126 DAB2
2227 KIAA1199
2127 HSPA5
2128 COL6A3
2129 HSP90B1
2130 SERPINH1
2131 ADAMTS1
2132 AXL
2133 TNFRSF12A
2134 KLF6
2135 ID2
2136 STC2
2137 CKAP4
2138 H3F3B
2139 ANKRD11
2140 ARID5B
2171 SLC38A2
2141 MEG3
2142 POSTN
2143 ITGB1
2144 VCAN
2145 RRBP1
2146 MTDH
2147 DKK1
2148 COL6A1
2149 THBS1
2150 SCUBE3
2151 PTX3
2152 ID1
2153 FBN1
2154 CTGF
2155 ID3
2156 COL3A1
2157 CYR61
2158 HIST1H4C
2159 COL1A2
2160 FN1
2161 NEAT1
2162 COL1A1
2163 MALAT1Negative markers
as.data.frame(mixture_neg) cluster p_val avg_logFC pct.1 pct.2 p_val_adj
2163 12 0.000000e+00 -3.4917593 0.955 1.000 0.000000e+00
2162 12 0.000000e+00 -2.4984584 0.573 1.000 0.000000e+00
2161 12 0.000000e+00 -2.4003554 0.154 0.992 0.000000e+00
2160 12 0.000000e+00 -2.1803482 0.617 0.998 0.000000e+00
2159 12 0.000000e+00 -2.1738990 0.571 0.999 0.000000e+00
2158 12 0.000000e+00 -1.8664315 0.304 0.944 0.000000e+00
2157 12 0.000000e+00 -1.7091193 0.203 0.953 0.000000e+00
2156 12 0.000000e+00 -1.6314050 0.207 0.963 0.000000e+00
2155 12 0.000000e+00 -1.5794227 0.527 0.996 0.000000e+00
2154 12 0.000000e+00 -1.4308999 0.270 0.865 0.000000e+00
2153 12 0.000000e+00 -1.4034415 0.174 0.964 0.000000e+00
2152 12 0.000000e+00 -1.2847646 0.322 0.921 0.000000e+00
2151 12 0.000000e+00 -1.2653708 0.335 0.865 0.000000e+00
2150 12 0.000000e+00 -1.2420304 0.259 0.813 0.000000e+00
2149 12 0.000000e+00 -1.2330423 0.129 0.679 0.000000e+00
2148 12 0.000000e+00 -1.1423616 0.311 0.969 0.000000e+00
2147 12 0.000000e+00 -1.1182616 0.197 0.751 0.000000e+00
2146 12 0.000000e+00 -1.1051841 0.429 0.974 0.000000e+00
2145 12 0.000000e+00 -1.0760617 0.287 0.952 0.000000e+00
2144 12 0.000000e+00 -1.0591907 0.144 0.904 0.000000e+00
2143 12 0.000000e+00 -1.0543828 0.758 0.999 0.000000e+00
2142 12 0.000000e+00 -1.0402266 0.181 0.587 0.000000e+00
2141 12 0.000000e+00 -1.0238471 0.116 0.884 0.000000e+00
2171 12 1.514850e-297 -1.0180213 0.061 0.872 3.647456e-293
2140 12 0.000000e+00 -1.0165932 0.156 0.891 0.000000e+00
2139 12 0.000000e+00 -1.0100344 0.243 0.946 0.000000e+00
2138 12 0.000000e+00 -0.9846268 0.724 0.998 0.000000e+00
2137 12 0.000000e+00 -0.9730315 0.369 0.968 0.000000e+00
2136 12 0.000000e+00 -0.9622743 0.192 0.849 0.000000e+00
2135 12 0.000000e+00 -0.9604329 0.262 0.884 0.000000e+00
2134 12 0.000000e+00 -0.9545360 0.092 0.854 0.000000e+00
2133 12 0.000000e+00 -0.9493460 0.752 0.917 0.000000e+00
2132 12 0.000000e+00 -0.9451443 0.442 0.930 0.000000e+00
2131 12 0.000000e+00 -0.9373251 0.090 0.784 0.000000e+00
2130 12 0.000000e+00 -0.9219611 0.381 0.966 0.000000e+00
2129 12 0.000000e+00 -0.9112763 0.562 0.986 0.000000e+00
2128 12 0.000000e+00 -0.9063511 0.188 0.881 0.000000e+00
2127 12 0.000000e+00 -0.9037984 0.327 0.908 0.000000e+00
2227 12 7.553348e-259 -0.8972211 0.064 0.648 1.818695e-254
2126 12 0.000000e+00 -0.8874138 0.382 0.940 0.000000e+00
2125 12 0.000000e+00 -0.8835162 0.582 0.977 0.000000e+00
2124 12 0.000000e+00 -0.8781101 0.566 0.984 0.000000e+00
2123 12 0.000000e+00 -0.8763949 0.817 0.949 0.000000e+00
2122 12 0.000000e+00 -0.8717619 0.551 0.795 0.000000e+00
2121 12 0.000000e+00 -0.8638207 0.629 0.982 0.000000e+00
2120 12 0.000000e+00 -0.8601576 0.552 0.971 0.000000e+00
2119 12 0.000000e+00 -0.8564741 0.640 0.972 0.000000e+00
2225 12 3.833156e-260 -0.8543148 0.160 0.545 9.229474e-256
2118 12 0.000000e+00 -0.8440326 0.335 0.780 0.000000e+00
2205 12 2.743689e-274 -0.8435958 0.169 0.607 6.606256e-270
2117 12 0.000000e+00 -0.8369631 0.242 0.888 0.000000e+00
2164 12 2.483470e-307 -0.8353496 0.094 0.843 5.979699e-303
2116 12 0.000000e+00 -0.8201162 0.157 0.797 0.000000e+00
2115 12 0.000000e+00 -0.8108053 0.130 0.741 0.000000e+00
2201 12 2.813645e-277 -0.8088716 0.097 0.825 6.774694e-273
2114 12 0.000000e+00 -0.7961270 0.449 0.882 0.000000e+00
2307 12 3.886550e-214 -0.7941424 0.090 0.540 9.358036e-210
2113 12 0.000000e+00 -0.7895862 0.400 0.791 0.000000e+00
2112 12 0.000000e+00 -0.7756508 0.133 0.793 0.000000e+00
2111 12 0.000000e+00 -0.7715693 0.169 0.844 0.000000e+00
2110 12 0.000000e+00 -0.7709099 0.158 0.857 0.000000e+00
2170 12 1.073760e-298 -0.7655769 0.146 0.695 2.585400e-294
2109 12 0.000000e+00 -0.7599929 0.243 0.847 0.000000e+00
2199 12 5.785917e-278 -0.7576467 0.090 0.828 1.393133e-273
2108 12 0.000000e+00 -0.7464335 0.909 1.000 0.000000e+00
2107 12 0.000000e+00 -0.7448708 0.365 0.861 0.000000e+00
2106 12 0.000000e+00 -0.7409302 0.131 0.788 0.000000e+00
2105 12 0.000000e+00 -0.7381918 0.236 0.887 0.000000e+00
2216 12 1.889672e-269 -0.7313916 0.434 0.847 4.549952e-265
2387 12 1.216527e-190 -0.7311709 0.039 0.807 2.929154e-186
2343 12 8.256766e-203 -0.7253824 0.543 0.840 1.988064e-198
2104 12 0.000000e+00 -0.7253784 0.371 0.916 0.000000e+00
2260 12 1.981316e-234 -0.7239916 0.074 0.793 4.770613e-230
2103 12 0.000000e+00 -0.7233920 0.212 0.842 0.000000e+00
2378 12 8.556079e-193 -0.7199610 0.045 0.747 2.060133e-188
2167 12 1.425591e-301 -0.7146120 0.234 0.724 3.432539e-297
2102 12 0.000000e+00 -0.7097213 0.558 0.979 0.000000e+00
2189 12 2.830588e-283 -0.7073061 0.116 0.795 6.815491e-279
2101 12 0.000000e+00 -0.7072108 0.835 0.999 0.000000e+00
2245 12 1.528740e-243 -0.7063975 0.419 0.804 3.680899e-239
2100 12 0.000000e+00 -0.7042925 0.354 0.867 0.000000e+00
2099 12 0.000000e+00 -0.7005891 0.421 0.935 0.000000e+00
2098 12 0.000000e+00 -0.6996461 0.183 0.763 0.000000e+00
2238 12 3.546340e-251 -0.6979157 0.348 0.734 8.538877e-247
2192 12 3.782550e-282 -0.6967576 0.111 0.795 9.107625e-278
2097 12 0.000000e+00 -0.6941179 0.317 0.905 0.000000e+00
2194 12 1.357946e-281 -0.6936349 0.124 0.817 3.269662e-277
2096 12 0.000000e+00 -0.6934495 0.246 0.868 0.000000e+00
2095 12 0.000000e+00 -0.6865198 0.730 0.995 0.000000e+00
2341 12 4.480356e-203 -0.6855900 0.046 0.645 1.078780e-198
2094 12 0.000000e+00 -0.6855268 0.386 0.917 0.000000e+00
2184 12 1.731055e-287 -0.6854173 0.129 0.812 4.168034e-283
2259 12 1.604078e-234 -0.6850852 0.072 0.798 3.862300e-230
2176 12 1.232868e-292 -0.6837251 0.118 0.800 2.968499e-288
2093 12 0.000000e+00 -0.6827244 0.865 1.000 0.000000e+00
2092 12 0.000000e+00 -0.6795942 0.171 0.843 0.000000e+00
2091 12 0.000000e+00 -0.6792095 0.750 0.975 0.000000e+00
2226 12 1.995339e-259 -0.6780798 0.399 0.779 4.804377e-255
2211 12 2.751543e-271 -0.6733764 0.115 0.810 6.625165e-267
2090 12 0.000000e+00 -0.6731121 0.354 0.850 0.000000e+00
2089 12 0.000000e+00 -0.6700642 0.335 0.899 0.000000e+00
2217 12 8.348527e-269 -0.6685944 0.120 0.799 2.010158e-264
2305 12 1.909946e-214 -0.6663756 0.130 0.559 4.598767e-210
2430 12 1.716208e-178 -0.6632414 0.035 0.559 4.132286e-174
2200 12 1.103356e-277 -0.6607071 0.128 0.772 2.656661e-273
2173 12 2.601412e-295 -0.6575380 0.297 0.772 6.263680e-291
2248 12 7.814237e-241 -0.6565571 0.108 0.674 1.881512e-236
2088 12 0.000000e+00 -0.6512030 0.249 0.822 0.000000e+00
2231 12 1.519055e-254 -0.6501797 0.601 0.924 3.657580e-250
2087 12 0.000000e+00 -0.6477677 0.771 0.979 0.000000e+00
2086 12 0.000000e+00 -0.6450464 0.827 0.999 0.000000e+00
2180 12 1.261491e-289 -0.6436512 0.176 0.746 3.037418e-285
2395 12 1.265895e-188 -0.6435194 0.047 0.647 3.048022e-184
2085 12 0.000000e+00 -0.6421550 0.669 0.992 0.000000e+00
2084 12 0.000000e+00 -0.6404564 0.198 0.809 0.000000e+00
2270 12 4.644787e-230 -0.6403940 0.092 0.683 1.118372e-225
2175 12 9.588183e-293 -0.6359800 0.212 0.746 2.308643e-288
2219 12 2.531172e-267 -0.6312435 0.117 0.784 6.094555e-263
2083 12 0.000000e+00 -0.6292587 0.260 0.815 0.000000e+00
2488 12 5.770768e-164 -0.6286257 0.041 0.626 1.389486e-159
2390 12 2.435324e-189 -0.6246703 0.060 0.551 5.863774e-185
2169 12 7.594470e-299 -0.6237574 0.168 0.760 1.828596e-294
2082 12 0.000000e+00 -0.6231384 0.326 0.880 0.000000e+00
2081 12 0.000000e+00 -0.6186290 0.555 0.940 0.000000e+00
2251 12 4.798737e-238 -0.6184027 0.622 0.902 1.155440e-233
2080 12 0.000000e+00 -0.6180724 0.400 0.884 0.000000e+00
2079 12 0.000000e+00 -0.6164725 0.853 1.000 0.000000e+00
2165 12 1.018225e-305 -0.6134389 0.238 0.773 2.451682e-301
2078 12 0.000000e+00 -0.6127770 0.778 0.999 0.000000e+00
2077 12 0.000000e+00 -0.6124966 0.855 0.995 0.000000e+00
2385 12 5.116654e-191 -0.6076887 0.154 0.496 1.231988e-186
2444 12 1.443264e-173 -0.6042141 0.068 0.494 3.475091e-169
2076 12 0.000000e+00 -0.6042065 0.630 0.970 0.000000e+00
2075 12 0.000000e+00 -0.6034878 0.877 0.943 0.000000e+00
2074 12 0.000000e+00 -0.6030883 0.578 0.971 0.000000e+00
2195 12 1.415921e-281 -0.5996144 0.183 0.778 3.409255e-277
2295 12 1.592925e-219 -0.5960159 0.095 0.739 3.835444e-215
2073 12 0.000000e+00 -0.5958696 0.278 0.844 0.000000e+00
2383 12 2.426446e-191 -0.5915972 0.065 0.586 5.842397e-187
2072 12 0.000000e+00 -0.5901048 0.540 0.940 0.000000e+00
2316 12 4.416315e-212 -0.5891716 0.213 0.597 1.063360e-207
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2998 12 6.267290e-24 0.3035860 0.992 0.995 1.509038e-19
3074 12 2.081265e-13 0.3039921 0.945 0.953 5.011269e-09
2989 12 2.140523e-26 0.3059965 0.998 0.996 5.153951e-22
2963 12 5.345145e-32 0.3076487 1.000 0.999 1.287004e-27
3120 12 2.338021e-08 0.3116574 0.922 0.933 5.629487e-04
3048 12 1.519755e-15 0.3122709 0.984 0.988 3.659266e-11
3066 12 4.737148e-14 0.3136689 0.584 0.486 1.140611e-09
3101 12 1.291977e-10 0.3154902 0.580 0.494 3.110823e-06
2964 12 8.161483e-32 0.3170956 1.000 1.000 1.965122e-27
3005 12 1.654523e-22 0.3178707 0.999 0.998 3.983759e-18
3125 12 7.784361e-08 0.3206946 0.628 0.535 1.874318e-03
3002 12 1.121855e-22 0.3218900 0.996 0.997 2.701201e-18
2931 12 2.213391e-48 0.3228607 0.505 0.375 5.329403e-44
3029 12 6.321913e-18 0.3231173 0.989 0.992 1.522190e-13
3145 12 7.876434e-07 0.3243332 0.867 0.860 1.896488e-02
3010 12 4.356853e-21 0.3244262 0.992 0.995 1.049043e-16
3108 12 5.301461e-10 0.3251004 0.968 0.962 1.276486e-05
3034 12 2.408529e-17 0.3258396 0.609 0.504 5.799257e-13
3136 12 2.249982e-07 0.3259449 0.626 0.677 5.417507e-03
3045 12 1.172597e-15 0.3264920 0.965 0.966 2.823378e-11
3053 12 3.568580e-15 0.3268396 0.980 0.980 8.592426e-11
3098 12 8.833803e-11 0.3268954 0.671 0.602 2.127003e-06
3111 12 8.229942e-10 0.3278067 0.942 0.971 1.981605e-05
3014 12 7.312598e-21 0.3319052 0.587 0.473 1.760727e-16
3016 12 1.867559e-20 0.3324909 0.998 0.998 4.496709e-16
2944 12 1.254186e-38 0.3356295 0.496 0.468 3.019828e-34
3075 12 2.220511e-13 0.3364133 0.625 0.535 5.346547e-09
3128 12 1.304268e-07 0.3374239 0.670 0.582 3.140417e-03
3032 12 1.865841e-17 0.3413163 0.646 0.546 4.492573e-13
3035 12 3.061773e-17 0.3415697 0.637 0.555 7.372136e-13
3065 12 4.478936e-14 0.3431447 0.979 0.994 1.078438e-09
3038 12 8.625236e-17 0.3433945 0.589 0.452 2.076784e-12
3122 12 3.580272e-08 0.3441122 0.975 0.981 8.620579e-04
3100 12 1.192820e-10 0.3444284 0.662 0.576 2.872073e-06
3088 12 1.721967e-11 0.3522546 0.486 0.386 4.146151e-07
3149 12 1.867606e-06 0.3525789 0.990 0.995 4.496822e-02
3000 12 1.252620e-23 0.3528214 0.612 0.485 3.016058e-19
3113 12 1.262379e-09 0.3531063 0.986 0.990 3.039556e-05
3130 12 1.615931e-07 0.3531152 0.965 0.972 3.890838e-03
3140 12 3.806657e-07 0.3538464 0.971 0.972 9.165668e-03
3117 12 2.327743e-09 0.3539942 0.980 0.971 5.604739e-05
3126 12 9.296161e-08 0.3552499 0.766 0.746 2.238330e-03
3104 12 2.215647e-10 0.3553449 0.982 0.983 5.334834e-06
3024 12 3.229280e-19 0.3573475 0.999 0.999 7.775460e-15
2979 12 3.394588e-28 0.3575394 0.464 0.362 8.173490e-24
2985 12 8.699300e-27 0.3579215 0.627 0.497 2.094617e-22
3114 12 1.634618e-09 0.3587551 0.724 0.695 3.935833e-05
3033 12 2.172623e-17 0.3628883 0.999 0.998 5.231241e-13
3006 12 3.787971e-22 0.3635997 1.000 1.000 9.120677e-18
3084 12 2.192866e-12 0.3654555 0.694 0.677 5.279983e-08
3092 12 2.641142e-11 0.3658475 0.712 0.608 6.359341e-07
3008 12 1.052502e-21 0.3671490 1.000 1.000 2.534214e-17
3077 12 3.621110e-13 0.3698627 0.678 0.574 8.718908e-09
3096 12 5.165760e-11 0.3700255 0.994 0.985 1.243812e-06
3131 12 1.780438e-07 0.3717544 0.992 0.995 4.286938e-03
3123 12 4.245716e-08 0.3775322 0.762 0.684 1.022283e-03
3037 12 8.435689e-17 0.3818124 1.000 1.000 2.031145e-12
3071 12 1.250544e-13 0.3819645 0.735 0.671 3.011061e-09
3055 12 6.790083e-15 0.3831854 0.481 0.362 1.634916e-10
3079 12 5.681444e-13 0.3837040 0.759 0.684 1.367978e-08
3069 12 6.209156e-14 0.3850962 0.703 0.602 1.495041e-09
2949 12 3.902009e-36 0.3872250 0.608 0.478 9.395258e-32
3133 12 1.949636e-07 0.3895233 0.790 0.728 4.694333e-03
2974 12 7.193629e-30 0.3940197 0.592 0.543 1.732082e-25
3118 12 3.676596e-09 0.3956879 1.000 0.994 8.852507e-05
3072 12 1.542686e-13 0.4032524 0.802 0.756 3.714479e-09
3132 12 1.911078e-07 0.4039756 0.998 0.993 4.601495e-03
3139 12 2.693748e-07 0.4113883 0.997 0.996 6.486006e-03
2922 12 1.750445e-55 0.4171685 0.605 0.431 4.214720e-51
3090 12 2.291553e-11 0.4174120 0.761 0.657 5.517601e-07
3011 12 4.574101e-21 0.4181667 0.755 0.686 1.101352e-16
3135 12 2.081912e-07 0.4208607 0.837 0.807 5.012827e-03
2911 12 1.291957e-62 0.4296550 0.533 0.504 3.110775e-58
3091 12 2.605415e-11 0.4339156 0.615 0.520 6.273318e-07
3124 12 6.012528e-08 0.4342427 0.643 0.552 1.447696e-03
3143 12 6.261107e-07 0.4363626 0.802 0.753 1.507549e-02
2943 12 9.517114e-39 0.4366635 0.755 0.639 2.291531e-34
2984 12 3.711328e-27 0.4372834 0.680 0.523 8.936136e-23
2971 12 3.001871e-30 0.4400096 0.720 0.596 7.227905e-26
2955 12 3.384281e-33 0.4452460 0.721 0.603 8.148672e-29
2991 12 5.014838e-26 0.4454430 0.746 0.618 1.207473e-21
3030 12 1.226800e-17 0.4503268 0.838 0.779 2.953890e-13
3142 12 4.113136e-07 0.4522879 0.886 0.835 9.903609e-03
3067 12 5.506404e-14 0.4525914 0.851 0.784 1.325832e-09
2980 12 4.597765e-28 0.4558981 0.586 0.605 1.107050e-23
3015 12 9.616198e-21 0.4566583 0.631 0.787 2.315388e-16
3013 12 6.402276e-21 0.4585287 0.813 0.725 1.541540e-16
2975 12 2.511764e-29 0.4625293 0.764 0.640 6.047824e-25
3026 12 8.901131e-19 0.4662484 0.806 0.726 2.143214e-14
3080 12 6.363857e-13 0.4672990 0.802 0.729 1.532289e-08
2972 12 6.399843e-30 0.4702569 0.650 0.508 1.540954e-25
3127 12 1.190792e-07 0.4702633 0.876 0.843 2.867189e-03
3115 12 2.014664e-09 0.4739975 0.893 0.823 4.850908e-05
2961 12 3.930541e-32 0.4759427 0.795 0.670 9.463956e-28
2952 12 1.732671e-34 0.4794895 0.749 0.643 4.171925e-30
3085 12 3.289698e-12 0.4828577 0.337 0.219 7.920935e-08
3040 12 4.998221e-16 0.4886329 0.855 0.780 1.203472e-11
2921 12 8.227271e-56 0.4902571 0.723 0.543 1.980962e-51
3097 12 6.576947e-11 0.4906259 0.869 0.789 1.583597e-06
3025 12 3.425821e-19 0.4956660 0.868 0.806 8.248693e-15
3083 12 9.872859e-13 0.4971301 0.815 0.758 2.377187e-08
3137 12 2.320430e-07 0.5051090 0.801 0.782 5.587131e-03
3003 12 1.151055e-22 0.5067382 0.817 0.817 2.771509e-18
2990 12 2.845356e-26 0.5083540 0.840 0.736 6.851049e-22
2967 12 1.356907e-31 0.5089915 0.860 0.770 3.267161e-27
3076 12 3.569818e-13 0.5116079 0.851 0.766 8.595408e-09
3089 12 1.990313e-11 0.5138625 0.907 0.852 4.792276e-07
3064 12 3.494068e-14 0.5153472 0.860 0.754 8.413016e-10
2948 12 9.090296e-37 0.5177514 0.803 0.691 2.188762e-32
3078 12 4.454335e-13 0.5185085 0.932 0.888 1.072515e-08
2945 12 1.046275e-37 0.5226878 0.838 0.747 2.519220e-33
2956 12 5.908923e-33 0.5229395 0.769 0.638 1.422751e-28
3119 12 5.204180e-09 0.5243551 0.925 0.858 1.253062e-04
3009 12 3.056596e-21 0.5290174 0.888 0.825 7.359672e-17
3041 12 5.471120e-16 0.5294783 0.940 0.915 1.317336e-11
2970 12 2.937228e-30 0.5299717 0.901 0.812 7.072257e-26
2996 12 3.481665e-24 0.5346733 0.853 0.756 8.383154e-20
3107 12 3.970132e-10 0.5365269 0.959 0.936 9.559283e-06
2924 12 4.366474e-51 0.5385950 0.808 0.644 1.051360e-46
2954 12 1.769469e-33 0.5421068 0.809 0.709 4.260527e-29
2965 12 1.164753e-31 0.5481752 0.888 0.834 2.804492e-27
3001 12 1.970257e-23 0.5506943 0.891 0.807 4.743984e-19
2950 12 1.723374e-35 0.5520658 0.847 0.750 4.149540e-31
3086 12 1.225189e-11 0.5535442 0.962 0.924 2.950009e-07
3106 12 3.621689e-10 0.5613670 0.943 0.900 8.720304e-06
3054 12 4.224262e-15 0.5650529 0.953 0.916 1.017118e-10
2959 12 1.249564e-32 0.5655426 0.804 0.735 3.008701e-28
2966 12 1.202318e-31 0.5728397 0.899 0.833 2.894942e-27
2946 12 5.560978e-37 0.5751532 0.900 0.821 1.338972e-32
3057 12 8.209262e-15 0.5757581 0.970 0.940 1.976626e-10
2957 12 6.578284e-33 0.5774421 0.909 0.806 1.583919e-28
3012 12 6.104583e-21 0.5794064 0.868 0.778 1.469861e-16
2926 12 2.864088e-50 0.5827137 0.839 0.715 6.896152e-46
3087 12 1.377813e-11 0.5844032 0.961 0.951 3.317498e-07
2936 12 4.843083e-46 0.5882979 0.878 0.784 1.166118e-41
3046 12 1.341752e-15 0.5960556 0.993 0.987 3.230670e-11
2988 12 2.140507e-26 0.6010164 0.898 0.898 5.153914e-22
3073 12 1.642908e-13 0.6029394 0.981 0.958 3.955795e-09
3036 12 4.762223e-17 0.6042620 0.968 0.930 1.146648e-12
3112 12 8.748348e-10 0.6045117 0.862 0.884 2.106427e-05
2992 12 1.575472e-25 0.6083947 0.939 0.880 3.793421e-21
3103 12 2.066554e-10 0.6086655 0.999 0.994 4.975849e-06
2997 12 3.896657e-24 0.6091090 0.888 0.916 9.382372e-20
2986 12 1.402561e-26 0.6092847 0.911 0.833 3.377087e-22
2932 12 9.820720e-48 0.6099372 0.858 0.758 2.364633e-43
2935 12 1.077740e-46 0.6127951 0.874 0.834 2.594982e-42
3039 12 4.789789e-16 0.6168885 0.983 0.962 1.153285e-11
2900 12 3.393774e-75 0.6361930 0.824 0.653 8.171529e-71
2978 12 2.268224e-28 0.6460210 0.966 0.947 5.461429e-24
3044 12 7.562375e-16 0.6506241 0.981 0.984 1.820869e-11
3070 12 6.429362e-14 0.6525017 0.999 0.996 1.548062e-09
3018 12 2.750064e-20 0.6572799 0.979 0.935 6.621605e-16
3129 12 1.602184e-07 0.6581014 0.998 0.998 3.857739e-03
3134 12 2.069039e-07 0.6590033 0.996 0.986 4.981832e-03
2968 12 2.287010e-31 0.6594054 0.946 0.841 5.506664e-27
3148 12 1.635820e-06 0.6635402 0.993 0.961 3.938726e-02
2995 12 2.732381e-25 0.6649891 0.981 0.937 6.579028e-21
2973 12 6.812614e-30 0.6655060 0.968 0.938 1.640341e-25
3028 12 1.130948e-18 0.6663717 0.965 0.945 2.723095e-14
2960 12 1.811726e-32 0.6779660 0.917 0.833 4.362275e-28
2918 12 6.388973e-59 0.6789562 0.764 0.762 1.538337e-54
2916 12 1.107699e-60 0.6830628 0.795 0.891 2.667118e-56
3019 12 3.456933e-20 0.6852300 0.969 0.949 8.323604e-16
3058 12 8.209677e-15 0.6923497 0.921 0.839 1.976726e-10
3051 12 2.029214e-15 0.6995125 1.000 1.000 4.885941e-11
2940 12 9.058510e-41 0.7076955 0.995 0.992 2.181108e-36
3059 12 1.426291e-14 0.7078997 0.997 1.000 3.434223e-10
2938 12 5.483953e-44 0.7110705 0.981 0.943 1.320426e-39
2917 12 8.428734e-60 0.7186755 0.920 0.947 2.029471e-55
2951 12 6.884296e-35 0.7222543 0.989 0.973 1.657601e-30
2976 12 9.166893e-29 0.7229113 0.993 0.989 2.207205e-24
2933 12 1.475592e-47 0.7234454 0.940 0.829 3.552929e-43
2962 12 4.484064e-32 0.7363554 0.997 0.992 1.079673e-27
2983 12 2.113612e-27 0.7468260 0.991 0.980 5.089154e-23
3116 12 2.214225e-09 0.7517954 0.995 0.975 5.331410e-05
2915 12 8.407361e-62 0.7699642 0.975 0.934 2.024324e-57
2958 12 9.505189e-33 0.7785246 1.000 1.000 2.288659e-28
2867 12 2.086724e-87 0.7792938 0.975 0.923 5.024414e-83
2934 12 8.759269e-47 0.7815058 0.987 0.982 2.109057e-42
2994 12 2.611599e-25 0.7905585 1.000 1.000 6.288208e-21
3138 12 2.683866e-07 0.8035485 0.996 0.980 6.462212e-03
2999 12 7.364136e-24 0.8062394 0.896 0.856 1.773137e-19
2937 12 3.802018e-44 0.8307130 0.996 0.996 9.154500e-40
2804 12 3.359547e-103 0.8326101 0.957 0.891 8.089116e-99
2807 12 1.161964e-102 0.8469319 0.946 0.869 2.797777e-98
2904 12 4.623468e-71 0.8486577 0.996 0.992 1.113239e-66
2893 12 1.082714e-77 0.8514443 1.000 0.998 2.606959e-73
2941 12 1.063143e-40 0.8551415 0.999 1.000 2.559835e-36
2977 12 1.187346e-28 0.8673550 0.986 0.975 2.858892e-24
2633 12 1.988425e-135 0.8709833 0.989 0.957 4.787729e-131
2942 12 3.926200e-39 0.8751378 0.999 0.999 9.453504e-35
2892 12 6.892859e-79 0.8757626 0.988 0.950 1.659663e-74
2891 12 6.932459e-81 0.8911547 0.972 0.936 1.669197e-76
2202 12 4.479297e-276 0.8987640 0.755 0.635 1.078525e-271
2912 12 1.982561e-62 0.9188733 0.990 0.956 4.773612e-58
2753 12 5.892383e-116 0.9223137 0.996 0.972 1.418768e-111
2910 12 3.887985e-65 0.9424130 0.999 0.989 9.361489e-61
2598 12 1.921461e-143 0.9514433 0.947 0.994 4.626494e-139
2813 12 1.497577e-101 0.9649495 1.000 0.987 3.605866e-97
2919 12 2.029038e-57 0.9742187 0.943 0.923 4.885517e-53
2812 12 1.189038e-101 0.9816995 0.996 0.968 2.862965e-97
2625 12 1.764444e-136 1.0859023 0.991 0.992 4.248428e-132
2608 12 6.905506e-140 1.1026415 1.000 0.999 1.662708e-135
2846 12 3.547151e-94 1.1430022 0.998 0.993 8.540829e-90
2255 12 8.614404e-235 1.2978399 1.000 1.000 2.074176e-230
2049 12 0.000000e+00 1.3327502 0.895 0.895 0.000000e+00
gene
2163 MALAT1
2162 COL1A1
2161 NEAT1
2160 FN1
2159 COL1A2
2158 HIST1H4C
2157 CYR61
2156 COL3A1
2155 ID3
2154 CTGF
2153 FBN1
2152 ID1
2151 PTX3
2150 SCUBE3
2149 THBS1
2148 COL6A1
2147 DKK1
2146 MTDH
2145 RRBP1
2144 VCAN
2143 ITGB1
2142 POSTN
2141 MEG3
2171 SLC38A2
2140 ARID5B
2139 ANKRD11
2138 H3F3B
2137 CKAP4
2136 STC2
2135 ID2
2134 KLF6
2133 TNFRSF12A
2132 AXL
2131 ADAMTS1
2130 SERPINH1
2129 HSP90B1
2128 COL6A3
2127 HSPA5
2227 KIAA1199
2126 DAB2
2125 MARCKS
2124 AHNAK
2123 PPP1R14B
2122 UBE2S
2121 LIMA1
2120 LOX
2119 TXNRD1
2225 MKI67
2118 HMGB2
2205 FST
2117 SRRM2
2164 COL5A2
2116 IER3
2115 COL4A1
2201 NR2F2
2114 CLDN11
2307 HAS2
2113 GREM1
2112 DUSP1
2111 CRIM1
2110 EMP1
2170 PTGIS
2109 PRRX2
2199 LRP1
2108 MT-CO2
2107 COL6A2
2106 COL4A2
2105 SON
2216 SERPINE2
2387 XIST
2343 IGFBP3
2104 APLP2
2260 AKAP9
2103 CDH2
2378 PDGFRA
2167 CRLF1
2102 FSTL1
2189 COL5A1
2101 MT-ATP6
2245 CKS2
2100 RHOBTB3
2099 RBM39
2098 CITED2
2238 CYP1B1
2192 CD248
2097 VIMP
2194 EXT1
2096 PRKDC
2095 CALR
2341 ADM
2094 ENG
2184 SPAG9
2259 PXDN
2176 LAMC1
2093 MT-CO3
2092 LOXL2
2091 TGFBI
2226 DCN
2211 PNISR
2090 LMO4
2089 PRRC2C
2217 CXXC5
2305 TNFRSF11B
2430 FOS
2200 HERPUD1
2173 INHBA
2248 FBLN2
2088 ALCAM
2231 TIMP3
2087 IGFBP7
2086 MT-CYB
2180 ISLR
2395 PPAP2B
2085 CALU
2084 SPOCK1
2270 IER2
2175 EVA1B
2219 VCL
2083 GOLIM4
2488 HEG1
2390 ELN
2169 CDC42EP3
2082 LMAN1
2081 ATF4
2251 SERPINE1
2080 MXRA8
2079 MT-ND4
2165 CEBPB
2078 MT-ND1
2077 CCDC80
2385 TOP2A
2444 ASPM
2076 TMED9
2075 BRI3
2074 P4HB
2195 ATP2B1
2295 XBP1
2073 TIMP2
2383 JUNB
2072 TLN1
2316 FGF5
2181 TMEM165
2398 CEBPD
2186 BTG1
2071 KRT10
2368 ZFP36L1
2208 ARGLU1
2070 CDV3
2267 NAV1
2230 CTDNEP1
2482 ZFP36L2
2168 NT5E
2197 N4BP2L2
2069 OSBPL8
2068 ERLEC1
2375 RGS4
2505 COL12A1
2297 GANAB
2174 TJP1
2362 JUN
2584 THBS2
2338 SULF1
2312 LTBP2
2178 PSAP
2274 NR3C1
2392 TNFRSF1A
2196 SEC61A1
2262 SLC16A3
2324 H1FX
2067 PRRX1
2066 EPS8
2372 NGF
2065 MT-ND2
2064 LOXL1
2243 TGOLN2
2063 EIF5
2929 IGFBP5
2242 DCBLD2
2317 PHLDA1
2268 USP1
2553 TPBG
2062 PDIA3
2061 MT-CO1
2409 VASN
2563 CCNL1
2508 AEBP1
2224 DDX17
2246 IL6ST
2060 SSR2
2525 TRAM2
2241 FRMD6
2416 EFEMP1
2059 MYH9
2182 PRSS23
2275 ZBTB38
2285 SDF2L1
2707 EGR1
2188 NCOR1
2240 CEP170
2221 GTF2I
2407 TPX2
2449 ARL6IP1
2512 OXTR
2198 PAFAH1B1
2339 RP11-572C15.6
2249 TAF7
2058 PDIA6
2286 NFE2L2
2380 BRD2
2265 MBNL2
2254 IGFBP6
2290 LPP
2690 PAPPA
2212 SRSF5
2282 KCTD20
2235 CD81
2057 GNAI2
2250 SMURF2
2548 ANKRD37
2264 PDIA4
2421 SRGAP1
2203 MICAL2
2218 EIF4G1
2895 KCNQ1OT1
2266 P4HA1
2459 B4GALT1
2263 TM9SF3
2301 BPTF
2450 CDH11
2278 TEAD1
2843 ZFHX4
2442 CTSC
2389 SLC1A5
2761 CENPF
2326 MYADM
2185 THRAP3
2257 BGN
2213 THY1
2313 PPP1R15A
2457 ATP2B4
2292 XPO1
2303 DLC1
2234 PPP1R12A
2236 MMP2
2056 SPARC
2875 HES1
2055 NFIC
2391 BRD4
2222 SCAF11
2179 CTSB
2427 EEA1
2207 FERMT2
2499 DDIT4
2434 TCF4
2223 BCLAF1
2327 ARF6
2355 ADAM12
2472 ATP13A3
2172 FOXP1
2358 MGAT1
2755 TM4SF1
2166 CD44
2310 WHSC1L1
2318 RBMS1
2648 GLG1
2529 PODXL
2277 RAD21
2244 RRAS
2519 NKTR
2420 KMT2E
2209 WASF2
2237 CLTC
2360 GPBP1
2287 CDC42EP1
2054 CD99
2053 HIF1A
2745 FAT1
2431 F2R
2403 ARHGAP29
2258 SMC3
2760 HIST1H1E
2777 HSPG2
2210 HP1BP3
2269 BASP1
2740 SQLE
2381 SLC3A2
2541 ANKRD28
2052 MRPL14
2239 LMO7
2281 PGRMC2
2433 MAT2A
2252 HNRNPD
2276 ASPH
2183 KPNB1
2429 RND3
2492 ITGA5
2272 MBNL1
2376 GALNT1
2820 ACAN
2352 ATF5
2617 F3
2335 QSOX1
2601 SLC38A1
2191 IGFBP4
2667 WSB1
2256 POP7
2402 DNAJC3
2382 TAF10
2344 SH2D4A
2296 PNN
2280 ADAM9
2300 ASAP1
2051 MT-ND5
2187 ZNF706
2349 CREB3L1
2423 ZFAND5
2261 BBX
2273 LRP10
2624 ITGAV
2682 BDNF
2816 UGCG
2361 TOR1AIP2
2247 RNPS1
2446 NFIB
2050 SIVA1
2885 MIDN
2177 PCBP1
2729 ZFP36
2565 PMP22
2193 SRRM1
2214 BSG
2328 FKBP10
2365 CCDC85B
2288 MLEC
2331 PCM1
2490 GADD45B
2204 LY6E
2356 LARP1
2397 ELL2
2481 ANKRD12
2611 ARHGAP35
2417 CTDSP2
2447 PLOD1
2283 SEC63
2215 CANX
2342 GOLGB1
2412 FGFR1
2320 DPYSL2
2364 HLA-A
2479 RHOB
2228 SRSF11
2366 KRCC1
2814 C1orf63
2780 TNRC6B
2551 CDKN1A
2432 FGF2
2308 EIF2AK4
2309 MYO1B
2588 SUZ12
2500 PNRC1
2406 ROCK2
2493 LUZP1
2631 VEGFC
2379 MACF1
2544 MIS18BP1
2463 TRIP11
2710 PKN2
2573 HMGXB4
2530 TGIF1
2293 HNRNPA0
2400 PLEC
2336 SHOC2
2306 RTF1
2393 HLA-C
2700 SERTAD2
2558 NSD1
2550 WAC
2506 CTBP2
2549 FOSL1
2659 LTBP1
2357 IFI16
2701 SLC20A1
2443 C19orf48
2504 USP9X
2647 ARID4B
2764 SEL1L
2537 ZNF148
2229 TRAM1
2386 GLS
2878 PI16
2546 TMPO
2363 TRA2B
2452 SNAI2
2220 DDX5
2340 SDF4
2353 STAT1
2503 JAGN1
2487 PLOD2
2284 YY1
2311 U2SURP
2291 DEK
2425 DHX36
2832 CEP350
2408 VMP1
2271 LUC7L3
2739 JADE1
2703 RIF1
2579 RNF145
2294 PHACTR2
2756 FGF7
2369 CLMP
2388 PAWR
2643 NRP1
2560 RBMS3
2714 KLF4
2497 CHD9
2735 MKNK2
2483 ASAP2
2441 GRN
2746 SCN9A
2626 EML4
2436 CHTOP
2599 RNF213
2695 GTSE1
2367 CLIP1
2862 ADAMTS6
2253 TPR
2437 HECTD1
2394 C5orf24
2683 NTN4
2354 GLIPR1
2451 CTSL
2322 SSR1
2870 HIST1H1B
2424 RBM27
2765 FYN
2469 SDF2
2600 SLC4A7
2370 HNRNPAB
2901 SLC7A11
2552 NCOA7
2835 KMT2A
2351 IKBIP
2763 LUM
2346 SHC1
2774 PLAGL1
2675 TACC1
2435 USP34
2419 RFC1
2411 RPN2
2770 AMOTL2
2518 SKIL
2496 PXDC1
2769 IL6
2464 CRELD2
2332 DST
2494 APP
2345 ZNF106
2668 CKAP2
2596 GOPC
2806 SETD5
2384 NNMT
2674 NIPBL
2590 MCL1
2535 MAP7D3
2641 TM9SF2
2531 HLA-B
2477 HTRA1
2329 YWHAG
2501 MFGE8
2465 MAP7D1
2575 CCDC88A
2751 TSC22D1
2589 PTPN14
2470 PPP4R2
2609 DSEL
2413 PPIG
2410 SPCS3
2426 RSRC2
2602 MMP14
2581 SEC24D
2414 ASCC3
2591 ABHD17A
2672 AFF4
2776 SEMA3C
2510 PRKAR2A
2533 PLAUR
2527 SLFN5
2439 UBE2R2
2485 UBE2M
2728 UBN1
2654 HOOK3
2630 USP22
2620 CDH13
2583 GGNBP2
2757 KLF3
2298 JTB
2461 AFAP1
2299 TAF1D
2640 ATXN2
2787 PIEZO1
2471 RALGPS2
2454 RSF1
2827 ZNF281
2561 CTBP1
2653 TSPAN5
2302 NEXN
2564 MYCBP2
2522 CHIC2
2373 LSM6
2724 CDK12
2882 RBBP6
2330 ENAH
2509 LINC00657
2871 ZNF503
2664 HHIP
2866 ANKRD1
2474 SPATS2
2526 SNHG7
2566 ASH1L
2815 LY6K
2903 FAM43A
2577 ITGB5
2399 MESDC2
2851 EPC1
2534 SLC39A7
2673 DDIT3
2323 CNPY2
2467 DNMT1
2348 MYOF
2741 ATOH8
2511 PPP2CB
2513 CEBPG
2347 GOLGA4
2772 RNF24
2845 TCF7L2
2725 HELLS
2206 RTN4
2637 ANKLE2
2502 BRD7
2325 ARL6IP5
2810 JMJD1C
2847 NUFIP2
2350 ZDHHC12
2555 DNAJC1
2456 CCM2
2428 RBFOX2
2861 EGFR
2314 VAT1
2779 PEAK1
2768 CLSTN1
2662 H2AFX
2671 ZNF22
2607 METRN
2831 POLR2A
2836 MRC2
2628 NABP1
2655 SRGN
2438 FAM120A
2860 NOTCH2
2418 SRSF7
2440 DNAJC10
2733 TENM3
2540 PCOLCE
2557 TBL1XR1
2785 ATP2A2
2698 CHD1
2656 SH3RF1
2279 SPATS2L
2574 PABPN1
2737 SEMA7A
2415 PLIN2
2738 TRIB3
2478 SMIM12
2841 AURKA
2521 RPN1
2863 VEPH1
2719 ADAM10
2523 RB1CC1
2333 TSPAN4
2458 PSMG3
2660 TSC22D4
2632 SVIL
2726 CREB3L2
2547 IMP3
2480 FNDC3B
2570 MPHOSPH8
2498 BDP1
2445 C19orf10
2829 MYC
2623 SENP6
2614 MARK3
2758 ANPEP
2319 ERP29
2568 SYNE1
2587 ANKIB1
2532 PARP1
2516 MIER1
2460 BCL7C
2594 HERC4
2619 HOXB2
2595 TAOK3
2794 CDC42EP2
2811 PRRC2A
2840 ZFC3H1
2645 NRBF2
2334 ACTN4
2455 GADD45A
2839 CENPA
2773 BMPR2
2833 SLC7A5
2604 ELOVL1
2889 ABL2
2720 PAM
2473 COPA
2809 RBM26
2585 FLNA
2556 SSBP4
2830 CENPE
2734 FADS3
2736 SACS
2872 PTPRF
2592 CCDC107
2791 REV3L
2786 FRMD4A
2684 CCDC12
2377 SFT2D1
2844 ATP1B1
2797 SGOL2
2718 TAOK1
2881 POLR2J3
2475 MAP2K2
2315 SSNA1
2822 CEP55
2517 HNRNPUL1
2520 CHD4
2289 FHL2
2627 CHD2
2783 TMEM87A
2616 PHF3
2857 LBR
2713 CSNK1E
2906 VEGFA
2669 SMAD5
2606 TRIP12
2495 RAD50
2680 RNMT
2748 ARHGAP21
2586 MPZL1
2902 G0S2
2767 TES
2850 IRF2BP2
2687 TGFBR2
2636 FAM63B
2337 DNAJC19
2603 SEPHS2
2681 TP53I11
2622 CTSZ
2484 DDX3X
2789 DBF4
2686 BAZ1A
2359 UBXN4
2536 APPL1
2613 P4HA2
2694 C1GALT1
2468 SURF4
2721 RRP36
2685 GNAQ
2666 MARCH7
2190 B2M
2515 CGGBP1
2795 NIN
2798 ABI3BP
2731 NXT1
2663 CBX6
2723 KAZALD1
2572 KRAS
2559 SCARB2
2799 TUSC1
2803 ERRFI1
2401 DDX24
2678 PTPN12
2404 MYO1C
2913 HOXA5
2582 AHCYL1
2821 SLC7A1
2580 RAB31
2696 SLC52A2
2793 METRNL
2716 ATP1A1
2524 C12orf44
2635 CHPF
2817 ECE1
2569 SS18L2
2629 CSNK1G3
2805 TRIO
2542 AMD1
2930 UNC5B
2567 UBE3A
2233 SSR3
2405 GNB1
2562 CD320
2634 TM2D2
2884 MEIS2
2858 KLF2
2610 SRSF4
2543 LRPAP1
2476 PLEKHJ1
2615 SETD5-AS1
2743 PLEKHO1
2766 PCYOX1
2898 TNRC6A
2855 ZBTB7A
2692 TMEM243
2605 VGLL3
2722 EIF4G3
2849 KIAA0947
2790 LEPREL4
2800 SETX
2796 TMEM259
2752 MGAT2
2754 KPNA6
2909 ZFHX3
2852 HMMR
2869 COL16A1
2448 LRRFIP1
2688 TMEM203
2689 TLK1
2554 PJA2
2873 RGMB
2864 AAK1
2321 NAA38
2489 FLYWCH2
2649 GCC2
2706 PHF14
2888 MAFG
2650 AGPAT2
2538 ACLY
2646 TEX264
2528 SORBS3
2856 ZKSCAN1
2819 ACSL3
2232 CD63
2665 FAM133B
2576 PHLDA3
2920 ZNF292
2879 HIST2H2AC
2744 VPS4B
2890 NFKBIA
2899 ARID1A
2762 HOXC8
2670 MANF
2657 CTSA
2775 ADAR
2651 KCMF1
2658 GPC1
2824 KDM5A
2639 TSSC4
2907 PDGFRB
2491 HDGF
2771 PHIP
2545 KATNBL1
2699 SLC39A6
2792 AKAP12
2859 PLAT
2705 FKBP9
2865 ARL4D
2711 SAT1
2727 SMCHD1
2808 FNBP4
2868 FILIP1L
2709 CCDC47
2677 TMEM30A
2887 EMILIN2
2612 C6orf62
2896 PGF
2759 HERC2
2747 MYH10
2652 UBE2J2
2374 MRPS12
2788 ATAD2
2742 EPB41L4A-AS1
2823 VPS13A
2883 RNF19A
2908 HIST1H1A
2396 ZYX
2717 LINC00667
2914 MAGI1
2732 SMPD1
2784 CALHM2
2621 PTEN
2371 RALBP1
2597 C11orf24
2486 HEBP2
2304 SEC62
2715 EGLN2
2578 CLINT1
2539 CCDC59
2642 SEC14L1
2894 PUM1
2834 SAMD11
2644 DESI2
2877 ARHGEF2
2712 SMC5
2638 DIAPH3
2818 SAV1
2618 MAP2K3
2453 ERGIC3
2704 PGP
2801 PRKCA
2462 LSM10
2702 NFIA
2750 PPP3CA
2676 YTHDC1
2874 TM2D3
2880 ATP10D
2923 RDH10
2828 SLC8A1
2876 AHR
2708 MBD4
2571 APH1A
2466 TMOD3
2693 PBRM1
2730 WAPAL
2679 CERCAM
2905 SCRG1
2848 KIF20B
2661 IFNGR2
2691 SLC25A37
2886 FBXO5
2781 COLGALT1
2593 ADD3
2782 PLOD3
2826 DHRS3
2507 DDX18
2838 MIA3
2778 NCBP2-AS2
2897 PIK3R1
2422 JAK1
2514 CBX5
2842 BIRC6
2853 TFRC
2928 FOSB
2854 PKD2
2802 HHIP-AS1
2825 MFAP2
2749 PURA
2697 CDC42BPB
2837 CDC25B
3121 MVP
2947 CALM2
3062 PDAP1
3031 MPC2
3022 SLIRP
2939 RPL38
3144 THOC7
3095 FIS1
3102 CCT3
2981 MINOS1
3109 ATP5D
3027 HNRNPC
3060 TAX1BP3
3082 TRAPPC1
3141 UBE2V2
3063 PTGES3
2925 RPL22
3147 PEPD
2953 COX8A
3017 S100A13
3081 CALM3
2982 RPS26
3043 CUTA
3099 HARS
3023 ATOX1
2969 TCEB2
3042 ARF1
3146 NAA10
3093 NDUFB11
3068 TMEM14C
3061 C4orf3
3050 C12orf75
3110 OSTF1
3052 COX7A2L
3047 EIF3E
3105 MRFAP1
3049 TXNDC17
3094 DDT
3021 COPS4
3056 UBC
3020 BRK1
2993 EDF1
2927 TRAK2
3004 BCCIP
2987 TMSB10
3007 UQCRQ
2998 CSTB
3074 LSM3
2989 UQCRH
2963 HINT1
3120 PFDN2
3048 ATP5G3
3066 ACAT1
3101 CAPG
2964 FAU
3005 COX7A2
3125 ACTR10
3002 ATP5L
2931 TSR2
3029 NDUFB2
3145 STMN1
3010 UBL5
3108 PEBP1
3034 DECR1
3136 PTPN11
3045 NDUFA11
3053 DBI
3098 NDUFA10
3111 NCL
3014 IDH3G
3016 CHCHD2
2944 PINK1
3075 CYB5B
3128 ADK
3032 PPA2
3035 RALB
3065 HMGB1
3038 FH
3122 RBX1
3100 CETN2
3088 CKB
3149 PABPC1
3000 HPRT1
3113 SUB1
3130 HSBP1
3140 ATPIF1
3117 PRDX5
3126 SDHB
3104 SHFM1
3024 NACA
2979 PSMC3IP
2985 HADHB
3114 HNRNPM
3033 BTF3
3006 RPL35
3084 PPP2R1A
3092 POLR2G
3008 TMSB4X
3077 PSMD13
3096 COX5B
3131 PSMA7
3123 RSU1
3037 RPL31
3071 PARVA
3055 HIST1H2BK
3079 MCTS1
3069 UCHL3
2949 ACOT7
3133 PSMD4
2974 HTATSF1
3118 PFDN5
3072 ADI1
3132 COX4I1
3139 COX7C
2922 ANXA4
3090 PRMT1
3011 ATP6V1E1
3135 GDI2
2911 KIF1C
3091 SLC9A3R2
3124 TYMS
3143 CCT2
2943 ETFA
2984 PSMC4
2971 UQCRC2
2955 PSME1
2991 ARL1
3030 SNRPC
3142 UBE2N
3067 ECHS1
2980 ZEB1
3015 UACA
3013 VAMP3
2975 VBP1
3026 PSMC3
3080 ANXA7
2972 PRPS1
3127 CAPN2
3115 RNF181
2961 COPS8
2952 MOCS2
3085 NEFM
3040 CAPZA2
2921 PPP1R7
3097 PSMB2
3025 PRDX3
3083 MIF
3137 TUBA1A
3003 CORO1C
2990 CMPK1
2967 SCP2
3076 MAP1LC3B
3089 PSMA1
3064 PSME2
2948 SDCBP
3078 ATP5C1
2945 GLO1
2956 ANXA6
3119 PSMA4
3009 MDH2
3041 PGAM1
2970 NDUFB6
2996 ESD
3107 SMS
2924 PSMC1
2954 CCT7
2965 ARPC4
3001 ATP5F1
2950 XRCC6
3086 C14orf166
3106 CLTA
3054 CAPZB
2959 HNRNPH3
2966 GHITM
2946 SDHC
3057 VDAC2
2957 COPS6
3012 CCT5
2926 CHMP5
3087 NME1
2936 GLRX3
3046 FKBP1A
2988 KIF5B
3073 CYCS
3036 CDC42
3112 LINC01133
2992 EIF3I
3103 TPI1
2997 HNRNPA3
2986 PSMD2
2932 CCT8
2935 TCEAL4
3039 ATP5J2
2900 MDH1
2978 YWHAQ
3044 HSPB1
3070 UQCRB
3018 MGST3
3129 RPS27L
3134 GSTP1
2968 PSMB3
3148 UBB
2995 PRDX6
2973 ATP5H
3028 SEPT7
2960 CSRP1
2918 PALLD
2916 MAP4
3019 COTL1
3058 UCHL1
3051 S100A6
2940 RHOA
3059 VIM
2938 GSTO1
2917 ANP32B
2951 ARPC3
2976 ENO1
2933 TALDO1
2962 ALDOA
2983 EIF4A1
3116 MYL9
2915 ARF4
2958 GAPDH
2867 VDAC1
2934 PKM
2994 S100A11
3138 TAGLN
2999 KRT7
2937 NPM1
2804 ATP5B
2807 PGK1
2904 ANXA5
2893 PPIA
2941 ACTG1
2977 CRYAB
2633 SNRPD2
2942 TPM1
2892 LDHB
2891 NQO1
2202 DYNC1LI2
2912 ANXA1
2753 SKP1
2910 MYL12A
2598 MAP1B
2813 MYL12B
2919 CCND1
2812 PRDX1
2625 LDHA
2608 ANXA2
2846 TPM2
2255 ACTB
2049 RAB13Top 10 positive markers
VlnPlot(all10x, features.plot=toupper(mixture_pos$gene[1:10]), group.by='res.0.5', point.size.use=-1, nCol=2, x.lab.rot=T, size.x.use=10)
Top 10 negative markers
VlnPlot(all10x, features.plot=toupper(mixture_neg$gene[1:10]), group.by='res.0.5', point.size.use=-1, nCol=2, x.lab.rot=T, size.x.use=10)
Plots
all10x@meta.data$mixture <- ifelse(all10x@meta.data$res.0.5==12, "mixture", "rest")
VlnPlot(all10x, features.plot=c('nGene', 'MALAT1', 'NEAT1', 'FN1', 'ITGB1', 'COL1A1', 'COL1A2', 'percent.mito'), group.by='mixture', point.size.use=-1, nCol=4)
Gene set enrichment
gsea_revigo <- read.table('tables/Revigo_mixture-cluster_cleaned.txt', header=T, sep='\t')
gsea_revigo revigo.term_ID
1 GO:0019674
2 GO:0006936
3 GO:0072524
4 GO:0007010
5 GO:0006090
6 GO:0006950
7 GO:0051186
8 GO:0009611
9 GO:0065008
10 GO:0051179
11 GO:0071840
12 GO:0032501
13 GO:0001775
14 GO:0030029
15 GO:0034109
16 GO:0017144
17 GO:0048869
18 GO:0032502
19 GO:0072593
20 GO:0016192
21 GO:0070671
22 GO:0002252
23 GO:0005975
24 GO:0034643
25 GO:0044403
revigo.description
1 NAD metabolic process
2 muscle contraction
3 pyridine-containing compound metabolic process
4 cytoskeleton organization
5 pyruvate metabolic process
6 response to stress
7 cofactor metabolic process
8 response to wounding
9 regulation of biological quality
10 localization
11 cellular component organization or biogenesis
12 multicellular organismal process
13 cell activation
14 actin filament-based process
15 homotypic cell-cell adhesion
16 drug metabolic process
17 cellular developmental process
18 developmental process
19 reactive oxygen species metabolic process
20 vesicle-mediated transport
21 response to interleukin-12
22 immune effector process
23 carbohydrate metabolic process
24 establishment of mitochondrion localization, microtubule-mediated
25 symbiosis, encompassing mutualism through parasitism
revigo.log10.p.value revigo.frequency gsea.query.size gsea.term.size
1 -5.8153 0.308% 50 72
2 -5.4584 0.066% 50 359
3 -4.9830 1.351% 50 150
4 -4.8962 0.786% 50 1235
5 -4.5406 0.817% 50 109
6 -4.3862 4.575% 50 3862
7 -3.6904 3.985% 50 533
8 -3.6696 0.127% 50 667
9 -3.5045 3.395% 50 3656
10 -3.0052 18.495% 50 6415
11 -2.5850 8.568% 50 6297
12 -2.5591 2.373% 50 7414
13 -2.5452 0.171% 50 1384
14 -2.4283 0.398% 50 714
15 -2.3830 0.015% 50 78
16 -2.1824 0.058% 50 757
17 -2.1355 1.896% 50 4270
18 -2.1296 2.812% 50 6212
19 -2.0419 0.282% 50 254
20 -1.8928 1.085% 50 1999
21 -1.6946 0.001% 50 50
22 -1.6635 0.185% 50 1222
23 -1.4895 5.260% 50 572
24 -1.4283 0.006% 50 19
25 -1.3915 0.168% 50 746
gsea.overlap.size gsea.p.value
1 7 1.53e-06
2 11 3.48e-06
3 8 1.04e-05
4 17 1.27e-05
5 7 2.88e-05
6 28 4.11e-05
7 11 2.04e-04
8 12 2.14e-04
9 26 3.13e-04
10 34 9.88e-04
11 33 2.60e-03
12 36 2.76e-03
13 15 2.85e-03
14 11 3.73e-03
15 5 4.14e-03
16 11 6.57e-03
17 26 7.32e-03
18 32 7.42e-03
19 7 9.08e-03
20 17 1.28e-02
21 4 2.02e-02
22 13 2.17e-02
23 9 3.24e-02
24 3 3.73e-02
25 10 4.06e-02
gsea.intersection
1 PKM,ENO1,PGK1,GAPDH,LDHB,LDHA,ALDOA
2 VIM,RHOA,ENO1,MYL9,MYL12A,CRYAB,MYL12B,TPM1,GSTO1,ALDOA,TPM2
3 PKM,ENO1,PGK1,GAPDH,LDHB,LDHA,ALDOA,TALDO1
4 VIM,MAP4,RHOA,ACTB,CRYAB,ARPC3,GAPDH,PALLD,MAP1B,ANXA1,DYNC1LI2,TPM1,RAB13,ALDOA,NPM1,ACTG1,TPM2
5 PKM,ENO1,PGK1,GAPDH,LDHB,LDHA,ALDOA
6 VIM,PKM,RHOA,ENO1,ACTB,MYL9,MYL12A,PGK1,COTL1,CRYAB,CCND1,GAPDH,SKP1,PRDX1,PRDX6,LDHA,ANXA1,TPM1,UCHL1,CSRP1,ANXA5,ARF4,UBB,NQO1,NPM1,ANXA2,ACTG1,VDAC1
7 PKM,ENO1,PGK1,GAPDH,LDHB,PRDX1,PRDX6,LDHA,GSTO1,ALDOA,TALDO1
8 PKM,RHOA,ACTB,MYL9,MYL12A,ANXA1,TPM1,CSRP1,ANXA5,ARF4,ANXA2,ACTG1
9 VIM,RHOA,ACTB,MYL9,MYL12A,CRYAB,CCND1,ARPC3,GAPDH,SKP1,PRDX1,PRDX6,MYL12B,SEPT7,MAP1B,ANXA1,TPM1,GSTO1,ALDOA,CSRP1,ANXA5,UBB,NQO1,NPM1,ANXA2,ACTG1
10 MAP4,PKM,RHOA,ACTB,MYL12A,COTL1,CRYAB,CCND1,ARPC3,GAPDH,SKP1,PRDX6,SNRPD2,PALLD,MAP1B,ANXA1,DYNC1LI2,ANP32B,TPM1,RAB13,GSTO1,ALDOA,UCHL1,S100A11,ANXA5,ATP5H,ARF4,UBB,NPM1,ANXA2,ACTG1,PPIA,S100A6,VDAC1
11 VIM,MAP4,PKM,RHOA,ENO1,ACTB,MYL12A,CRYAB,ARPC3,GAPDH,SKP1,MYL12B,SEPT7,SNRPD2,PALLD,MAP1B,ANXA1,DYNC1LI2,ANP32B,TPM1,RAB13,ALDOA,UCHL1,ATP5H,ARF4,UBB,NPM1,ANXA2,ACTG1,PPIA,S100A6,TPM2,VDAC1
12 VIM,MAP4,PKM,RHOA,ENO1,ACTB,MYL9,MYL12A,PGK1,CRYAB,CCND1,GAPDH,PRDX1,MYL12B,SEPT7,PALLD,MAP1B,LDHA,ANXA1,KRT7,ANP32B,TPM1,RAB13,GSTO1,TAGLN,ALDOA,UCHL1,CSRP1,ANXA5,ARF4,UBB,ANXA2,ACTG1,S100A6,TPM2,VDAC1
13 PKM,RHOA,ACTB,MYL9,MYL12A,COTL1,PRDX1,PRDX6,ANXA1,ALDOA,CSRP1,S100A11,ANXA2,ACTG1,PPIA
14 VIM,RHOA,ACTB,ARPC3,PALLD,ANXA1,TPM1,RAB13,ALDOA,ACTG1,TPM2
15 ACTB,MYL9,MYL12A,CSRP1,ACTG1
16 PKM,RHOA,ENO1,PGK1,GAPDH,PRDX1,PRDX6,LDHA,ALDOA,ATP5H,NQO1
17 VIM,MAP4,RHOA,MYL9,MYL12A,PGK1,CCND1,MYL12B,SEPT7,PALLD,MAP1B,ANXA1,KRT7,ANP32B,TPM1,RAB13,TAGLN,ALDOA,UCHL1,ARF4,UBB,NPM1,ANXA2,ACTG1,S100A6,VDAC1
18 VIM,MAP4,PKM,RHOA,ACTB,MYL9,MYL12A,PGK1,CRYAB,CCND1,PRDX1,MYL12B,SEPT7,PALLD,MAP1B,LDHA,ANXA1,KRT7,ANP32B,TPM1,RAB13,TAGLN,ALDOA,UCHL1,ARF4,UBB,NQO1,NPM1,ANXA2,ACTG1,S100A6,VDAC1
19 RHOA,CRYAB,PRDX1,PRDX6,ARF4,NQO1,VDAC1
20 PKM,RHOA,ACTB,COTL1,ARPC3,PRDX6,ANXA1,DYNC1LI2,RAB13,ALDOA,S100A11,ANXA5,ARF4,UBB,ANXA2,ACTG1,PPIA
21 GSTO1,TALDO1,ANXA2,PPIA
22 PKM,RHOA,ACTB,COTL1,ARPC3,PRDX1,PRDX6,ANXA1,ALDOA,S100A11,ANXA2,ACTG1,PPIA
23 PKM,ENO1,PGK1,GAPDH,LDHB,LDHA,GSTO1,ALDOA,TALDO1
24 MAP1B,UCHL1,UBB
25 VIM,RHOA,GAPDH,KRT7,EIF4A1,UBB,NPM1,ANXA2,PPIA,VDAC1Nr of cells
Sample composition in cluster 12.
cluster12 <- SubsetData(all10x, cells.use=rownames(all10x@meta.data)[which(all10x@meta.data$res.0.5 %in% 12)])
rotate_x <- function(data, column_to_plot, labels_vec, rot_angle) {
plt <- barplot(data[[column_to_plot]], col='steelblue', xaxt="n")
text(plt, par("usr")[3], labels = labels_vec, srt = rot_angle, adj = c(1.1,1.1), xpd = TRUE, cex=1)
}
rotate_x((cluster12@meta.data %>% count(sample_name))[,2], 'n', as.vector(unlist((cluster12@meta.data %>% count(sample_name))[,1])), 45)
scmap results
TSNEPlot(all10x, group.by='predicted_labels_fat', pt.size=0.1)
Add line breaks for legend
all10x@meta.data$predicted_labels_fat_breaks = as.vector(all10x@meta.data$predicted_labels_fat)
all10x@meta.data$predicted_labels_fat_breaks[which(all10x@meta.data$predicted_labels_fat == 'mesenchymal stem cell of adipose')] = 'mesenchymal\nstem cell\nof adipose'
all10x@meta.data$predicted_labels_fat_breaks[which(all10x@meta.data$predicted_labels_fat == 'smooth muscle cell')] = 'smooth\nmuscle cell'TSNEPlot(all10x, group.by='predicted_labels_fat_breaks', pt.size=0.1) + theme(legend.key.height=unit(1, "cm"))
Stressed cell analysis
stress_genes <- read.table('/raid5/projects/timshel/sc-arc_lira/src/data-genelists/171219-van_den_Brink2017-genes_affected_by_dissociation.csv', header=T) %>% pull(1)
length(stress_genes)[1] 140stress_genes [1] Actg1 Btg1 Cxcl1 Dnajb4 Errfi1 H3f3b Hspb1
[8] Irf1 Klf6 Mir22hg Nfkbia Pcf11 Pxdc1 Sdc4
[15] Srf Tpm3 Usp2 Gadd45g Ankrd1 Btg2 Cyr61
[22] Dusp1 Fam132b Hipk3 Hsph1 Irf8 Klf9 Mt1
[29] Nfkbiz Pde4b Rap1b Serpine1 Srsf5 Tppp3 Wac
[36] Hspe1 Arid5a Ccnl1 Dcn Dusp8 Fos Hsp90aa1
[43] Id3 Itpkc Litaf Mt2 Nop58 Per1 Rassf1
[50] Skil Srsf7 Tra2a Zc3h12a Ier5 Atf3 Ccrn4l
[57] Ddx3x Egr1 Fosb Hsp90ab1 Idi1 Jun Lmna
[64] Myadm Nppc Phlda1 Rhob Slc10a6 Stat3 Tra2b
[71] Zfand5 Kcne4 Atf4 Cebpb Ddx5 Egr2 Fosl2
[78] Hspa1a Ier2 Junb Maff Myc Nr4a1 Pnp
[85] Rhoh Slc38a2 Tagln2 Trib1 Zfp36 Bag3 Cebpd
[92] Des Eif1 Gadd45a Hspa1b Ier3 Jund Mafk
[99] Myd88 Odc1 Pnrc1 Ripk1 Slc41a1 Tiparp Tubb4b
[106] Zfp36l1 Bhlhe40 Cebpg Dnaja1 Eif5 Gcc1 Hspa5
[113] Ifrd1 Klf2 Mcl1 Nckap5l Osgin1 Ppp1cc Sat1
[120] Socs3 Tnfaip3 Tubb6 Zfp36l2 Brd2 Csrnp1 Dnajb1
[127] Erf Gem Hspa8 Il6 Klf4 Midn Ncoa7
[134] Oxnad1 Ppp1r15a Sbno2 Sqstm1 Tnfaip6 Ubc Zyx
140 Levels: Actg1 Ankrd1 Arid5a Atf3 Atf4 Bag3 Bhlhe40 Brd2 Btg1 ... Zyxde_genes <- read.table('output/markergenes/180504/markers_10x-180504_res.0.5_negbinom', header=T)
de_genes <- de_genes[de_genes$p_val_adj < 0.05,]Cluster 12 is the mixture cluster. Check markers MALAT1 and NEAT1 to be sure:
VlnPlot(all10x, group.by='res.0.5', features.plot=c('MALAT1', 'NEAT1'), point.size.use =-1)
Are any of the stress genes in the DE genes for the mixture cluster?
de_genes_pos <- de_genes[de_genes$avg_logFC > 0, ]
de_genes_neg <- de_genes[de_genes$avg_logFC < 0, ]
intersect_pos <- list()
intersect_neg <- list()
n_pos <- list()
n_neg <- list()
perc_pos <- list()
perc_neg <- list()
for (i in unique(de_genes$cluster)){
c <- paste('cluster', i)
genes_pos <- de_genes_pos[de_genes_pos$cluster == i, 'gene']
genes_neg <- de_genes_neg[de_genes_neg$cluster == i, 'gene']
intersect_pos[[c]] <- length(intersect(toupper(stress_genes), genes_pos))
intersect_neg[[c]] <- length(intersect(toupper(stress_genes), genes_neg))
n_pos[[c]] <- length(genes_pos)
n_neg[[c]] <- length(genes_neg)
perc_pos[[c]] <- (intersect_pos[[c]] / n_pos[[c]]) * 100
perc_neg[[c]] <- (intersect_neg[[c]] / n_neg[[c]]) * 100
}
stressed_cells <- data.frame(
shared.pos.genes=unlist(intersect_pos),
shared.neg.genes=unlist(intersect_neg),
n_pos=unlist(n_pos),
n_neg=unlist(n_neg),
perc_pos=unlist(perc_pos),
perc_neg=unlist(perc_neg)
)
stressed_cells <- stressed_cells[order(rownames(stressed_cells)),]
stressed_cells shared.pos.genes shared.neg.genes n_pos n_neg perc_pos
cluster 0 1 7 91 87 1.098901
cluster 1 7 31 308 867 2.272727
cluster 10 5 5 95 68 5.263158
cluster 11 7 11 157 327 4.458599
cluster 12 3 54 252 849 1.190476
cluster 13 12 23 322 529 3.726708
cluster 14 10 27 341 516 2.932551
cluster 2 2 5 125 135 1.600000
cluster 3 4 13 50 252 8.000000
cluster 4 21 3 281 119 7.473310
cluster 5 22 10 210 275 10.476190
cluster 6 3 3 148 71 2.027027
cluster 7 20 7 370 147 5.405405
cluster 8 9 4 182 47 4.945055
cluster 9 3 1 51 129 5.882353
perc_neg
cluster 0 8.0459770
cluster 1 3.5755479
cluster 10 7.3529412
cluster 11 3.3639144
cluster 12 6.3604240
cluster 13 4.3478261
cluster 14 5.2325581
cluster 2 3.7037037
cluster 3 5.1587302
cluster 4 2.5210084
cluster 5 3.6363636
cluster 6 4.2253521
cluster 7 4.7619048
cluster 8 8.5106383
cluster 9 0.77519383 of the 140 genes were found in the positive markers for the mixture cluster, 54 in the negative numbers. Similar numbers were found for the other clusters in the data. These results indicate that the mixture cluster does not consist of stressed cells.
Figures for report
get_violin_plot <- function(x){
return(VlnPlot(all10x, features.plot=c(x), point.size.use=-1, group.by='mixture', size.title.use=14, remove.legend=T) + theme(axis.title.x=element_blank()))
}
fig2_first_row <- plot_grid(
TSNEPlot(all10x, group.by='sample_name', pt.size=0.1),
TSNEPlot(all10x, group.by='predicted_labels_fat_breaks', pt.size=0.1) + theme(legend.key.height=unit(1, "cm")),
labels=c('a', 'b'), rel_widths=c(48/100, 52/100)
)
fig2_violin <- plot_grid(
get_violin_plot('nGene'),
get_violin_plot('MALAT1'),
get_violin_plot('NEAT1'),
get_violin_plot('FN1'),
get_violin_plot('ITGB1'),
get_violin_plot('COL1A1'),
get_violin_plot('COL1A2'),
get_violin_plot('percent.mito'),
labels=c('d', 'e', 'f', 'g', 'h', 'i', 'j', 'k'), nrow=2
)
fig2_barplot <- plot_grid(ggplot(data=cluster12@meta.data %>% count(sample_name), aes(x=sample_name, y=n)) +
geom_bar(stat="identity", position='dodge') +
scale_y_continuous(expand=c(0,0)) +
theme(axis.line.y=element_blank(), axis.ticks.y=element_blank(), axis.title.x=element_blank(), axis.title.y=element_blank()) +
coord_flip(), labels=c('c'))
fig2_second_row <- plot_grid(fig2_barplot, fig2_violin, rel_widths=c(2/8, 6/8))
fig2 <- plot_grid(
fig2_first_row,
fig2_second_row,
nrow=2
)
fig2
save_plot("plots/180504_mixture.pdf", fig2, base_width=12, base_height=9)# get_violin_plot <- function(x){
# return(VlnPlot(all10x, features.plot=c(x), point.size.use=-1, group.by='mixture', size.title.use=14, remove.legend=T) + theme(axis.title.x=element_blank()))
# }
#
# fig2_first_row <- plot_grid(
# TSNEPlot(all10x, group.by='sample_name', pt.size=0.1) + theme(legend.position=c(0.1, 0.5), legend.key = element_blank(), legend.background= element_rect(fill=alpha('white', 0.8), size=0.5, linetype='solid', colour=alpha('black', 0.3))),
# DimPlot(all10x, reduction.use='tsne', cells.highlight = rownames(all10x@meta.data)[all10x@meta.data$res.0.5 == 12], cols.highlight='blue', cols.use='gray', pt.size=0.1),
# labels=c('a', 'b')
# )
#
# fig2_violin <- plot_grid(
# get_violin_plot('nGene'),
# get_violin_plot('MALAT1'),
# get_violin_plot('NEAT1'),
# get_violin_plot('FN1'),
# get_violin_plot('ITGB1'),
# get_violin_plot('COL1A1'),
# get_violin_plot('COL1A2'),
# get_violin_plot('percent.mito'),
# labels=c('d', 'e', 'f', 'g', 'h', 'i', 'j', 'k'), nrow=2
# )
#
# fig2_barplot <- plot_grid(ggplot(data=cluster12@meta.data %>% count(sample_name), aes(x=sample_name, y=n)) +
# geom_bar(stat="identity", position='dodge') +
# scale_y_continuous(expand=c(0,0)) +
# theme(axis.line.y=element_blank(), axis.ticks.y=element_blank(), axis.title.x=element_blank(), axis.title.y=element_blank()) +
# coord_flip(), labels=c('c'))
#
# fig2_second_row <- plot_grid(fig2_barplot, fig2_violin, rel_widths=c(2/8, 6/8))
#
# fig2 <- plot_grid(
# fig2_first_row,
# fig2_second_row,
# nrow=2
# )
#
# fig2
#
# #save_plot("plots/180504_mixture.pdf", fig2, base_width=12, base_height=10)write.table(stressed_cells, 'tables/10x-180504-stressed-cells-analysis.txt', sep='\t')Session information
sessionInfo()R version 3.4.3 (2017-11-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Storage
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bindrcpp_0.2.2 gProfileR_0.6.6 Seurat_2.3.4 Matrix_1.2-14
[5] cowplot_0.9.3 ggplot2_3.0.0 dplyr_0.7.6
loaded via a namespace (and not attached):
[1] Rtsne_0.13 colorspace_1.3-2 class_7.3-14
[4] modeltools_0.2-22 ggridges_0.5.0 mclust_5.4.1
[7] rprojroot_1.3-2 htmlTable_1.12 base64enc_0.1-3
[10] rstudioapi_0.7 proxy_0.4-22 flexmix_2.3-14
[13] bit64_0.9-7 mvtnorm_1.0-8 codetools_0.2-15
[16] splines_3.4.3 R.methodsS3_1.7.1 robustbase_0.93-2
[19] knitr_1.20 Formula_1.2-3 jsonlite_1.5
[22] workflowr_1.1.1 ica_1.0-2 cluster_2.0.7-1
[25] kernlab_0.9-27 png_0.1-7 R.oo_1.22.0
[28] compiler_3.4.3 httr_1.3.1 backports_1.1.2
[31] assertthat_0.2.0 lazyeval_0.2.1 lars_1.2
[34] acepack_1.4.1 htmltools_0.3.6 tools_3.4.3
[37] igraph_1.2.2 gtable_0.2.0 glue_1.3.0
[40] RANN_2.6 reshape2_1.4.3 Rcpp_0.12.18
[43] trimcluster_0.1-2.1 gdata_2.18.0 ape_5.1
[46] nlme_3.1-137 iterators_1.0.10 fpc_2.1-11.1
[49] gbRd_0.4-11 lmtest_0.9-36 stringr_1.3.1
[52] irlba_2.3.2 gtools_3.8.1 DEoptimR_1.0-8
[55] MASS_7.3-50 zoo_1.8-3 scales_1.0.0
[58] doSNOW_1.0.16 parallel_3.4.3 RColorBrewer_1.1-2
[61] yaml_2.2.0 reticulate_1.10 pbapply_1.3-4
[64] gridExtra_2.3 rpart_4.1-13 segmented_0.5-3.0
[67] latticeExtra_0.6-28 stringi_1.2.4 foreach_1.4.4
[70] checkmate_1.8.5 caTools_1.17.1.1 bibtex_0.4.2
[73] Rdpack_0.9-0 SDMTools_1.1-221 rlang_0.2.2
[76] pkgconfig_2.0.2 dtw_1.20-1 prabclus_2.2-6
[79] bitops_1.0-6 evaluate_0.11 lattice_0.20-35
[82] ROCR_1.0-7 purrr_0.2.5 bindr_0.1.1
[85] labeling_0.3 htmlwidgets_1.2 bit_1.1-14
[88] tidyselect_0.2.4 plyr_1.8.4 magrittr_1.5
[91] R6_2.2.2 snow_0.4-2 gplots_3.0.1
[94] Hmisc_4.1-1 pillar_1.3.0 whisker_0.3-2
[97] foreign_0.8-70 withr_2.1.2 fitdistrplus_1.0-9
[100] mixtools_1.1.0 survival_2.42-6 nnet_7.3-12
[103] tsne_0.1-3 tibble_1.4.2 crayon_1.3.4
[106] hdf5r_1.0.0 KernSmooth_2.23-15 rmarkdown_1.10
[109] grid_3.4.3 data.table_1.11.4 git2r_0.23.0
[112] metap_1.0 digest_0.6.15 diptest_0.75-7
[115] tidyr_0.8.1 R.utils_2.7.0 stats4_3.4.3
[118] munsell_0.5.0 This reproducible R Markdown analysis was created with workflowr 1.1.1