##Ascite
library(dplyr)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionfoldChange=2
pvalue=0.05
rt <- read.table("ascite.txt",header=T,check.names=F)
DEG <- rt[with(rt,(abs(logFC) > foldChange & PValue < pvalue)),]
DEG <- DEG[order(DEG$PValue),]
DEG <-select(DEG,sample, logFC, PValue)
row.names(DEG) <- 1:nrow(DEG)
DEG## sample logFC PValue
## 1 hsa-miR-1246 6.219958 3.550000e-12
## 2 hsa-miR-1290 5.050441 3.050000e-09
## 3 hsa-miR-9-5p -4.764249 1.090000e-08
## 4 hsa-miR-1269b 5.830616 1.130000e-06
## 5 hsa-miR-7847-3p -3.987814 7.420000e-06
## 6 hsa-miR-508-3p -3.844457 8.730000e-06
## 7 hsa-miR-141-5p 4.379654 9.560000e-06
## 8 hsa-miR-671-5p 3.844647 1.390000e-05
## 9 hsa-miR-1269a 5.168545 1.420000e-05
## 10 hsa-miR-202-3p -4.208955 1.740000e-05
## 11 hsa-miR-892a -4.516332 2.380000e-05
## 12 hsa-miR-877-3p -3.627006 2.510000e-05
## 13 hsa-miR-1227-3p -4.523706 3.000000e-05
## 14 hsa-miR-934 4.919667 3.070000e-05
## 15 hsa-miR-204-3p -3.224399 3.070000e-05
## 16 hsa-miR-1296-5p 4.056537 3.950000e-05
## 17 hsa-miR-4745-5p 4.600229 4.630000e-05
## 18 hsa-miR-34b-3p -4.245500 4.670000e-05
## 19 hsa-miR-7107-5p -3.679007 5.750000e-05
## 20 hsa-miR-4646-3p -3.903716 7.150000e-05
## 21 hsa-miR-34c-5p -3.343482 7.490000e-05
## 22 hsa-miR-513c-5p -3.530362 7.620000e-05
## 23 hsa-miR-514a-3p -3.362747 7.890000e-05
## 24 hsa-miR-7111-3p -3.703896 1.085780e-04
## 25 hsa-miR-200c-3p 2.924482 1.187810e-04
## 26 hsa-miR-4710 -3.764241 1.196250e-04
## 27 hsa-miR-150-5p 3.558014 1.303370e-04
## 28 hsa-miR-202-5p -3.539676 1.338630e-04
## 29 hsa-miR-4658 4.051577 1.382650e-04
## 30 hsa-miR-516a-5p 4.172371 1.388200e-04
## 31 hsa-miR-4739 -3.855642 1.427930e-04
## 32 hsa-miR-130b-3p 3.325294 1.503730e-04
## 33 hsa-miR-4649-5p -3.950415 1.616990e-04
## 34 hsa-miR-4716-5p -3.906021 1.696690e-04
## 35 hsa-miR-184 -3.217633 1.921900e-04
## 36 hsa-miR-6880-3p -3.672766 1.932980e-04
## 37 hsa-miR-4459 -3.519631 2.009210e-04
## 38 hsa-miR-6856-5p -3.914651 2.123130e-04
## 39 hsa-miR-34c-3p -3.706319 2.649180e-04
## 40 hsa-miR-4780 4.225190 2.702630e-04
## 41 hsa-miR-203b-3p 3.928113 2.827190e-04
## 42 hsa-miR-514a-5p -3.746747 2.841400e-04
## 43 hsa-miR-6780b-3p -3.565345 3.193250e-04
## 44 hsa-miR-129-5p -2.933953 4.287810e-04
## 45 hsa-miR-6741-5p -3.530664 4.981400e-04
## 46 hsa-miR-6727-3p -3.601187 5.728660e-04
## 47 hsa-miR-10a-3p 2.647186 5.777710e-04
## 48 hsa-miR-320e 2.913574 6.014740e-04
## 49 hsa-miR-4664-3p 3.527311 6.488490e-04
## 50 hsa-miR-3654 3.923983 6.633080e-04
## 51 hsa-miR-141-3p 2.645840 7.909480e-04
## 52 hsa-miR-509-3-5p -2.803169 7.929760e-04
## 53 hsa-miR-2115-5p 3.840473 8.156530e-04
## 54 hsa-miR-6741-3p -3.361491 1.049877e-03
## 55 hsa-miR-937-3p 3.533167 1.054109e-03
## 56 hsa-miR-6884-3p -3.417916 1.057340e-03
## 57 hsa-miR-513a-3p -3.127173 1.130938e-03
## 58 hsa-miR-509-3p -2.694101 1.181754e-03
## 59 hsa-miR-618 3.545041 1.247824e-03
## 60 hsa-miR-513c-3p -3.162755 1.282909e-03
## 61 hsa-miR-139-5p -2.512083 1.406471e-03
## 62 hsa-miR-6510-5p -2.976562 1.416338e-03
## 63 hsa-miR-2115-3p 3.475781 1.811453e-03
## 64 hsa-miR-153-3p -3.038276 1.948397e-03
## 65 hsa-miR-1275 -2.826258 2.049883e-03
## 66 hsa-miR-483-5p 2.317392 2.159460e-03
## 67 hsa-miR-4758-3p 3.460514 2.181050e-03
## 68 hsa-miR-3127-3p 3.454887 2.243882e-03
## 69 hsa-miR-449a -2.834101 2.346507e-03
## 70 hsa-miR-1224-3p -3.100101 2.346800e-03
## 71 hsa-miR-139-3p -2.651907 2.361363e-03
## 72 hsa-miR-548az-5p 3.170167 2.380460e-03
## 73 hsa-miR-522-3p 3.419737 2.393427e-03
## 74 hsa-miR-145-5p -2.526510 2.458910e-03
## 75 hsa-miR-6850-5p 3.355928 2.467796e-03
## 76 hsa-miR-423-5p -2.046911 2.567477e-03
## 77 hsa-miR-4743-5p -2.941325 2.606267e-03
## 78 hsa-miR-3184-3p -2.042891 2.614207e-03
## 79 hsa-miR-6823-3p -3.073924 2.614368e-03
## 80 hsa-miR-6766-3p -3.068464 2.669491e-03
## 81 hsa-miR-3940-5p -2.967814 2.882236e-03
## 82 hsa-miR-324-3p -2.690686 3.118543e-03
## 83 hsa-miR-497-5p -2.706403 3.196072e-03
## 84 hsa-miR-1226-3p 3.286026 3.466416e-03
## 85 hsa-miR-660-3p -2.609477 3.478004e-03
## 86 hsa-miR-4741 3.070957 3.504098e-03
## 87 hsa-miR-4728-5p -2.959687 3.518421e-03
## 88 hsa-miR-1248 3.074419 3.744927e-03
## 89 hsa-miR-217 -2.746009 3.749126e-03
## 90 hsa-miR-378e -2.250062 4.053049e-03
## 91 hsa-miR-3154 -2.788372 4.064998e-03
## 92 hsa-miR-3180-5p 3.065830 4.169681e-03
## 93 hsa-miR-200a-5p 2.421567 4.209923e-03
## 94 hsa-miR-3911 2.976662 4.226246e-03
## 95 hsa-miR-675-5p 2.353811 4.351574e-03
## 96 hsa-miR-3615 2.350346 4.476105e-03
## 97 hsa-miR-4769-3p -2.850861 4.579465e-03
## 98 hsa-miR-4667-3p -2.861487 4.652243e-03
## 99 hsa-miR-4443 -2.119599 4.678821e-03
## 100 hsa-miR-378d -2.084540 4.829881e-03
## 101 hsa-miR-3180-3p 2.506186 4.993099e-03
## 102 hsa-miR-3611 -2.704452 5.022278e-03
## 103 hsa-miR-3180 2.836043 5.226948e-03
## 104 hsa-miR-429 2.264483 5.469393e-03
## 105 hsa-miR-3944-3p 3.077690 5.507376e-03
## 106 hsa-miR-449b-5p -2.759744 5.595717e-03
## 107 hsa-miR-3187-3p 2.752503 5.768186e-03
## 108 hsa-miR-3173-5p 3.036669 6.025374e-03
## 109 hsa-miR-6734-5p -2.452370 6.100578e-03
## 110 hsa-miR-7110-3p -2.723166 6.410387e-03
## 111 hsa-miR-6788-5p -2.478427 7.178357e-03
## 112 hsa-miR-664a-3p -2.412004 7.310648e-03
## 113 hsa-miR-4788 2.904915 7.685907e-03
## 114 hsa-miR-3131 -2.708520 7.693629e-03
## 115 hsa-miR-6809-5p -2.383813 8.332817e-03
## 116 hsa-miR-1270 2.614921 8.588600e-03
## 117 hsa-miR-3127-5p 2.529894 8.662777e-03
## 118 hsa-miR-507 -2.392237 8.866886e-03
## 119 hsa-miR-523-5p 2.819601 9.240474e-03
## 120 hsa-miR-6090 -2.608288 9.272659e-03
## 121 hsa-miR-506-3p -2.540148 9.296230e-03
## 122 hsa-miR-4449 2.708676 9.486290e-03
## 123 hsa-miR-4535 -2.509722 9.691027e-03
## 124 hsa-miR-508-5p -2.445539 9.717938e-03
## 125 hsa-miR-135b-5p 2.125703 9.760048e-03
## 126 hsa-miR-4787-5p -2.168413 1.011788e-02
## 127 hsa-miR-4716-3p -2.535847 1.028109e-02
## 128 hsa-miR-514b-3p -2.393938 1.032517e-02
## 129 hsa-miR-3960 -2.081973 1.080497e-02
## 130 hsa-miR-3162-3p -2.481411 1.086819e-02
## 131 hsa-miR-449c-5p -2.502871 1.116256e-02
## 132 hsa-miR-519a-5p 2.734028 1.124497e-02
## 133 hsa-miR-1247-3p -2.409642 1.149696e-02
## 134 hsa-miR-200b-5p 2.090883 1.169367e-02
## 135 hsa-miR-4758-5p 2.566745 1.218572e-02
## 136 hsa-miR-30b-3p -2.209708 1.218592e-02
## 137 hsa-miR-93-5p 2.005086 1.263520e-02
## 138 hsa-miR-1183 -2.464251 1.288164e-02
## 139 hsa-miR-641 2.405330 1.308513e-02
## 140 hsa-miR-6747-3p 2.638523 1.314385e-02
## 141 hsa-miR-4724-5p 2.526001 1.362515e-02
## 142 hsa-miR-6790-3p -2.317552 1.399187e-02
## 143 hsa-miR-6826-5p -2.328095 1.401733e-02
## 144 hsa-miR-6891-3p -2.326887 1.410823e-02
## 145 hsa-miR-203a-5p 2.633242 1.410990e-02
## 146 hsa-miR-6073 2.043734 1.440838e-02
## 147 hsa-miR-1291 -2.205515 1.496553e-02
## 148 hsa-miR-675-3p 2.346271 1.554591e-02
## 149 hsa-miR-6769b-5p -2.415237 1.576188e-02
## 150 hsa-miR-519c-5p 2.531166 1.628239e-02
## 151 hsa-miR-3529-5p 2.494824 1.757094e-02
## 152 hsa-miR-4479 2.399117 1.791689e-02
## 153 hsa-miR-378g -2.067312 1.797116e-02
## 154 hsa-miR-4485-3p -2.260608 1.834837e-02
## 155 hsa-miR-3677-3p 2.457920 1.863609e-02
## 156 hsa-miR-6730-3p 2.475321 1.885801e-02
## 157 hsa-miR-6124 -2.213538 1.899247e-02
## 158 hsa-miR-301b-5p -2.143801 1.950386e-02
## 159 hsa-miR-6891-5p -2.231616 2.070263e-02
## 160 hsa-miR-362-5p -2.058964 2.073008e-02
## 161 hsa-miR-6732-3p -2.196892 2.129273e-02
## 162 hsa-miR-6848-5p -2.209483 2.134586e-02
## 163 hsa-miR-1249-5p -2.251782 2.227197e-02
## 164 hsa-miR-518e-5p 2.379938 2.268266e-02
## 165 hsa-miR-154-5p -2.078047 2.278415e-02
## 166 hsa-miR-3660 2.380397 2.284150e-02
## 167 hsa-miR-223-3p 2.015908 2.287422e-02
## 168 hsa-miR-383-5p -2.103427 2.339203e-02
## 169 hsa-miR-6507-3p -2.187155 2.342637e-02
## 170 hsa-miR-5187-5p -2.054160 2.419418e-02
## 171 hsa-miR-3910 -2.088905 2.540679e-02
## 172 hsa-miR-1273d 2.286008 2.585159e-02
## 173 hsa-miR-765 -2.171122 2.611936e-02
## 174 hsa-miR-519b-5p 2.293813 2.615545e-02
## 175 hsa-miR-1273g-5p 2.314147 2.642912e-02
## 176 hsa-miR-3976 2.233568 2.693608e-02
## 177 hsa-miR-668-3p -2.081481 2.700611e-02
## 178 hsa-miR-548ar-3p -2.004025 2.830917e-02
## 179 hsa-miR-3198 2.229350 2.855194e-02
## 180 hsa-miR-3129-3p -2.032139 2.908813e-02
## 181 hsa-miR-3065-5p 2.136138 2.925714e-02
## 182 hsa-miR-6731-3p -2.137959 2.953440e-02
## 183 hsa-miR-5196-3p -2.153877 2.978374e-02
## 184 hsa-miR-6797-3p 2.164143 2.993712e-02
## 185 hsa-miR-6820-5p 2.205488 3.093773e-02
## 186 hsa-miR-6785-3p -2.127760 3.111301e-02
## 187 hsa-miR-6740-5p -2.002424 3.133800e-02
## 188 hsa-miR-942-5p 2.055642 3.216918e-02
## 189 hsa-miR-4800-3p 2.158659 3.241755e-02
## 190 hsa-miR-6892-3p -2.122002 3.258195e-02
## 191 hsa-miR-211-3p 2.179422 3.314440e-02
## 192 hsa-miR-1283 2.143460 3.483467e-02
## 193 hsa-miR-1273e 2.124273 3.493086e-02
## 194 hsa-miR-4718 2.129211 3.592455e-02
## 195 hsa-miR-6879-5p -2.001602 3.729119e-02
## 196 hsa-miR-885-5p 2.053535 3.739708e-02
## 197 hsa-miR-1470 -2.072351 3.815922e-02
## 198 hsa-miR-6800-5p 2.075113 3.935259e-02
## 199 hsa-miR-3181 2.093655 3.999468e-02
## 200 hsa-miR-5695 2.094384 4.011918e-02
## 201 hsa-miR-1253 2.099211 4.227282e-02
## 202 hsa-miR-7844-5p 2.020596 4.251460e-02
## 203 hsa-miR-4729 2.074527 4.379128e-02
## 204 hsa-miR-6877-5p 2.011368 4.463333e-02
## 205 hsa-miR-346 2.018900 4.494489e-02##Plasma
library(dplyr)
foldChange=2
pvalue=0.05
rt <- read.table("plasma.txt",header=T,check.names=F)
DEG <- rt[with(rt,(abs(logFC) > foldChange & PValue < pvalue)),]
DEG <- DEG[order(DEG$PValue),]
DEG <-select(DEG,sample,logFC, PValue)
row.names(DEG) <- 1:nrow(DEG)
DEG## sample logFC PValue
## 1 hsa-miR-192-3p -3.732483 0.000000279
## 2 hsa-miR-378c -2.200145 0.000000457
## 3 hsa-miR-378d -2.173337 0.000000971
## 4 hsa-miR-1269b -4.376035 0.000003930
## 5 hsa-miR-1290 2.868324 0.000004290
## 6 hsa-miR-34c-5p -3.718732 0.000005630
## 7 hsa-miR-5093 -2.920634 0.000005630
## 8 hsa-miR-34b-3p -3.391196 0.000006000
## 9 hsa-miR-196b-3p -2.192818 0.000007850
## 10 hsa-miR-1246 3.314221 0.000015200
## 11 hsa-miR-133b -2.978955 0.000016100
## 12 hsa-miR-7107-3p -2.391261 0.000017000
## 13 hsa-miR-4776-3p -2.051517 0.000019900
## 14 hsa-miR-296-3p 2.537006 0.000020000
## 15 hsa-miR-380-5p -2.063157 0.000024900
## 16 hsa-miR-3168 -2.271358 0.000030300
## 17 hsa-miR-3620-3p -2.336056 0.000031600
## 18 hsa-miR-1288-5p -3.575719 0.000031700
## 19 hsa-miR-455-3p -3.382359 0.000032300
## 20 hsa-miR-483-5p 2.655479 0.000037100
## 21 hsa-miR-31-3p -2.981006 0.000037100
## 22 hsa-miR-4254 -2.142337 0.000038000
## 23 hsa-miR-7113-3p -2.229213 0.000039900
## 24 hsa-miR-103a-2-5p -2.506243 0.000046500
## 25 hsa-miR-6856-3p -2.013670 0.000047200
## 26 hsa-miR-345-3p -2.649190 0.000056800
## 27 hsa-miR-133a-3p -2.463284 0.000062200
## 28 hsa-miR-122-3p -3.127767 0.000063400
## 29 hsa-miR-4433b-3p 2.691615 0.000065200
## 30 hsa-miR-6875-3p -2.015330 0.000067600
## 31 hsa-miR-4763-5p -2.197997 0.000067900
## 32 hsa-miR-615-3p 3.756966 0.000080800
## 33 hsa-miR-708-5p -2.725851 0.000085400
## 34 hsa-miR-5584-3p -2.298430 0.000087200
## 35 hsa-miR-6857-5p -2.030792 0.000091500
## 36 hsa-miR-130a-5p -2.028167 0.000097200
## 37 hsa-miR-6866-3p -2.119465 0.000100621
## 38 hsa-miR-4780 -2.183244 0.000101588
## 39 hsa-miR-6774-3p -2.283103 0.000107752
## 40 hsa-miR-3148 -2.109833 0.000113270
## 41 hsa-miR-6858-3p -2.039567 0.000113846
## 42 hsa-miR-194-3p -2.875272 0.000114807
## 43 hsa-miR-875-5p -2.045940 0.000114812
## 44 hsa-miR-145-5p -2.514085 0.000117199
## 45 hsa-miR-6511b-3p -2.100385 0.000121555
## 46 hsa-miR-4478 -2.126864 0.000124917
## 47 hsa-miR-5009-3p -2.043276 0.000137216
## 48 hsa-miR-3609 -2.185361 0.000138553
## 49 hsa-miR-1226-5p -2.133475 0.000142185
## 50 hsa-miR-675-5p 2.741083 0.000145820
## 51 hsa-miR-302a-5p -2.038460 0.000150297
## 52 hsa-miR-3683 -2.039399 0.000150946
## 53 hsa-miR-3182 -2.845483 0.000165624
## 54 hsa-miR-1470 -2.233718 0.000166592
## 55 hsa-miR-4314 -2.239844 0.000167186
## 56 hsa-miR-573 -2.052623 0.000171324
## 57 hsa-miR-449a -2.663299 0.000175555
## 58 hsa-miR-4477b -2.018288 0.000176949
## 59 hsa-miR-4632-3p -2.751524 0.000197660
## 60 hsa-miR-4474-5p -2.142368 0.000201438
## 61 hsa-miR-31-5p -2.677281 0.000209438
## 62 hsa-miR-5701 -2.785992 0.000209695
## 63 hsa-miR-7846-3p -2.159206 0.000210959
## 64 hsa-miR-320e 2.653592 0.000232248
## 65 hsa-miR-3653-5p -2.202626 0.000242483
## 66 hsa-miR-199b-5p -2.814214 0.000244624
## 67 hsa-miR-4324 -2.126222 0.000258594
## 68 hsa-miR-3129-5p -2.065705 0.000272622
## 69 hsa-miR-8059 -2.033843 0.000280584
## 70 hsa-miR-3193 -2.436610 0.000284706
## 71 hsa-miR-4312 -2.009485 0.000299163
## 72 hsa-miR-4667-3p -2.279018 0.000308502
## 73 hsa-miR-3941 -2.083020 0.000334987
## 74 hsa-miR-6728-3p -2.138435 0.000339559
## 75 hsa-miR-1247-3p -2.120025 0.000395385
## 76 hsa-miR-584-3p -2.213819 0.000396442
## 77 hsa-miR-203b-3p -2.545941 0.000408320
## 78 hsa-miR-8062 -2.032098 0.000418652
## 79 hsa-miR-3670 -2.112092 0.000428291
## 80 hsa-miR-6505-3p -2.245300 0.000429301
## 81 hsa-miR-6774-5p -2.130588 0.000494884
## 82 hsa-miR-6773-5p -2.251720 0.000505119
## 83 hsa-miR-3653-3p -2.128305 0.000525030
## 84 hsa-miR-362-5p -2.216927 0.000531469
## 85 hsa-miR-202-5p -2.471848 0.000544328
## 86 hsa-miR-802 -2.530448 0.000560830
## 87 hsa-miR-6832-3p -2.205994 0.000606252
## 88 hsa-miR-499a-5p 2.532729 0.000622117
## 89 hsa-miR-4699-5p -2.173338 0.000643445
## 90 hsa-miR-5581-5p -2.052002 0.000644580
## 91 hsa-miR-1299 -2.302702 0.000655534
## 92 hsa-miR-3607-3p -2.198192 0.000663919
## 93 hsa-miR-384 -2.022826 0.000671554
## 94 hsa-miR-216a-3p -2.098257 0.000675328
## 95 hsa-miR-210-5p -2.013891 0.000690805
## 96 hsa-miR-6810-3p -2.306437 0.000690896
## 97 hsa-miR-204-3p 2.525331 0.000745874
## 98 hsa-miR-412-3p -2.275065 0.000820918
## 99 hsa-miR-6747-5p -2.044639 0.000835255
## 100 hsa-miR-30c-2-3p -2.217034 0.000840429
## 101 hsa-miR-6789-3p -2.015610 0.000899212
## 102 hsa-miR-4791 -2.508807 0.000915534
## 103 hsa-miR-3651 -2.134947 0.000962109
## 104 hsa-miR-921 -2.075045 0.000969984
## 105 hsa-miR-3180-3p 2.593702 0.001166933
## 106 hsa-miR-4709-3p -2.110176 0.001337234
## 107 hsa-miR-133a-5p -2.038563 0.001595915
## 108 hsa-miR-5684 -2.299726 0.001611977
## 109 hsa-miR-1236-3p -2.082725 0.001701638
## 110 hsa-miR-4793-5p -2.066841 0.001749899
## 111 hsa-miR-8058 -2.011107 0.001829154
## 112 hsa-miR-429 2.052685 0.001884251
## 113 hsa-miR-6734-3p -2.045161 0.002124299
## 114 hsa-miR-502-5p 2.917984 0.002134632
## 115 hsa-miR-4782-5p -2.162467 0.002965393
## 116 hsa-miR-3159 -2.069401 0.003099166
## 117 hsa-miR-1273e -2.099872 0.003425896
## 118 hsa-miR-1224-5p 2.012802 0.003543199
## 119 hsa-miR-935 -2.275904 0.004037362
## 120 hsa-miR-6879-3p -2.168605 0.005175244
## 121 hsa-miR-1244 -2.075710 0.007588181
## 122 hsa-miR-4660 -2.111203 0.010916274
## 123 hsa-miR-4461 2.229124 0.015272890
## 124 hsa-miR-607 -2.186429 0.024572261
## 125 hsa-miR-4281 -2.193287 0.030041312
## 126 hsa-miR-4646-3p 2.535260 0.032924767