Identifier Base Mean log2 Fold Change Standard Error p-value Adjusted p-value
hsa-miR-3065-5p 4.548 -0.6188 0.2772 0.02563 0.09902
hsa-miR-137 3.249 -0.8998 0.351 0.01035 0.05129
hsa-miR-490-5p 3.273 -0.9614 0.3727 0.009898 0.04979
hsa-miR-95-5p 0.7177 -1.006 0.3404 0.003127 0.02424
hsa-miR-30e-5p 2745 0.4362 0.1551 0.00492 0.0321
hsa-miR-503-5p 0.626 0.9555 0.4254 0.02468 0.09623
hsa-miR-873-3p 53.67 -0.6712 0.2854 0.01867 0.07706
hsa-miR-487b-3p 7.533 -0.6254 0.2627 0.01731 0.07311
hsa-miR-1197 0.7815 -0.9415 0.3882 0.0153 0.06768
hsa-miR-518e-3p 4.466 0.6918 0.2825 0.01434 0.0643
hsa-miR-708-3p 17.41 -0.7665 0.2337 0.00104 0.01318
hsa-miR-451a 1057 -0.8394 0.2836 0.003082 0.02418
hsa-miR-377-5p 9.875 -0.9029 0.2634 0.0006087 0.00872
hsa-miR-1911-3p 60.61 0.637 0.2258 0.004789 0.03156
hsa-miR-132-5p 3.591 -0.9581 0.2302 3.168e-05 0.001305
hsa-miR-485-5p 35.37 -1.052 0.2866 0.000241 0.00467
hsa-miR-628-5p 3.087 -0.9161 0.2892 0.001535 0.01646
hsa-miR-4665-5p 0.835 0.9035 0.3768 0.0165 0.07107
hsa-miR-4454 283.7 -0.817 0.3264 0.01232 0.05757
hsa-miR-1298-3p 1600 0.6357 0.2278 0.005263 0.034
hsa-miR-760 14.68 -0.9508 0.2322 4.212e-05 0.001425
hsa-miR-136-3p 69.79 -0.9724 0.2205 1.036e-05 0.0005947
hsa-miR-181c-3p 106.2 -0.3896 0.1779 0.02852 0.1074
hsa-miR-574-3p 215.9 0.477 0.1864 0.01051 0.05169
hsa-miR-128-3p 213.8 -0.6376 0.241 0.008146 0.04522
hsa-miR-376a-5p 1.961 -0.8226 0.3019 0.006441 0.03894
hsa-miR-139-3p 2.776 -1.081 0.3629 0.002892 0.02324
hsa-miR-125b-2-3p 799.7 -0.2372 0.113 0.03581 0.1229
hsa-miR-409-5p 3.647 -0.8309 0.3672 0.02365 0.09331
hsa-miR-6875-5p 0.54 -1.035 0.4082 0.01127 0.05421
hsa-miR-4781-3p 0.5172 0.884 0.3421 0.00976 0.04948
hsa-miR-376c-3p 10.96 -0.7983 0.2981 0.007414 0.04211
hsa-miR-487a-5p 0.4755 -1.126 0.3922 0.004086 0.02865
hsa-miR-100-5p 6392 -0.4942 0.2283 0.03039 0.112
hsa-miR-30d-5p 6880 0.4926 0.1657 0.002957 0.02348
hsa-miR-193b-3p 29.39 -0.4864 0.2255 0.03099 0.1133
hsa-miR-145-3p 22.54 -0.5723 0.244 0.019 0.07775
hsa-miR-122-5p 34.77 -1.027 0.2533 4.978e-05 0.001491
hsa-miR-496 0.8402 -1.296 0.3633 0.0003602 0.006247
hsa-miR-148a-5p 187.5 0.5025 0.184 0.006324 0.03859
hsa-miR-124-3p 207.9 -1.75 0.2978 4.212e-09 2.776e-06
hsa-miR-433-3p 10.89 -0.8672 0.2885 0.002645 0.02193
hsa-miR-127-5p 13.93 -1.076 0.2447 1.083e-05 0.0005947
hsa-miR-654-3p 17.75 -0.4918 0.2309 0.03323 0.1159
hsa-miR-5683 1.77 -0.7173 0.3327 0.03111 0.1133
hsa-miR-5588-5p 0.556 0.8909 0.3471 0.01026 0.05122
hsa-miR-641 3.693 0.7797 0.26 0.00271 0.02205
hsa-miR-767-5p 249.8 0.6422 0.2194 0.003425 0.02565
hsa-miR-431-3p 7.541 -1.119 0.2844 8.372e-05 0.002299
hsa-miR-181b-5p 1139 -0.6425 0.2055 0.001767 0.01791
hsa-miR-1299 11.75 -0.9604 0.2964 0.001196 0.01389
hsa-miR-381-3p 53.91 -1.162 0.261 8.457e-06 0.0005947
hsa-miR-138-5p 79.82 -1.553 0.2807 3.144e-08 1.036e-05
hsa-miR-769-3p 2.687 -1.208 0.3125 0.0001113 0.002717
hsa-miR-30a-5p 22540 0.4198 0.1372 0.002218 0.02059
hsa-miR-549a 12.66 -0.6347 0.2602 0.01472 0.06556
hsa-miR-495-3p 7.134 -1.195 0.3045 8.726e-05 0.0023
hsa-miR-382-5p 9.042 -0.6891 0.2428 0.004538 0.03029
hsa-miR-664b-5p 0.4498 -0.7041 0.3401 0.03842 0.1272
hsa-miR-3928-3p 1.647 -0.6519 0.2862 0.02272 0.09075
hsa-miR-299-3p 2.432 -0.8994 0.3446 0.009046 0.04769
hsa-miR-432-5p 58.6 -0.6778 0.2533 0.007456 0.04211
hsa-miR-448 360 0.4508 0.2052 0.02801 0.1063
hsa-miR-655-3p 0.9868 -0.9749 0.3766 0.009636 0.04948
hsa-miR-3200-3p 13.85 -0.7638 0.2201 0.0005191 0.008146
hsa-miR-378h 0.4571 1.09 0.4011 0.006598 0.03917
hsa-miR-1303 2.168 0.4398 0.2102 0.0364 0.1243
hsa-miR-151a-5p|hsa-miR-151b 801.2 -0.3716 0.1492 0.01273 0.05868
hsa-miR-105-5p 27.12 0.6072 0.227 0.007477 0.04211
hsa-miR-323a-3p 45.24 -0.8022 0.2491 0.001282 0.01456
hsa-miR-33b-5p 16.34 -0.7845 0.2597 0.002521 0.02186
hsa-miR-30c-1-3p 22.04 0.4521 0.146 0.001965 0.01904
hsa-let-7f-5p 9888 0.5798 0.1901 0.00229 0.02096
hsa-miR-1296-5p 23.12 -0.9864 0.2563 0.0001191 0.002804
hsa-miR-16-2-3p 8.098 -0.5346 0.2564 0.03708 0.1256
hsa-miR-153-3p 16.8 -0.6382 0.2677 0.01715 0.07294
hsa-miR-490-3p 5.992 -0.7758 0.3235 0.01648 0.07107
hsa-miR-95-3p 9.356 -1.01 0.2448 3.682e-05 0.001355
hsa-miR-181a-5p 13000 -0.6418 0.17 0.0001597 0.003394
hsa-miR-3065-3p 4.169 -0.7356 0.2501 0.003271 0.02478
hsa-miR-30b-5p 366.7 0.4354 0.1961 0.02636 0.101
hsa-miR-518f-3p 2.66 0.7492 0.3257 0.02145 0.08619
hsa-miR-1306-3p 0.6994 -0.9156 0.3965 0.02093 0.08514
hsa-miR-452-5p 6.175 -0.6093 0.2434 0.01232 0.05757
hsa-miR-377-3p 1.174 -0.8889 0.3069 0.00378 0.02736
hsa-miR-146a-5p 916.1 -0.5983 0.2027 0.003165 0.02425
hsa-miR-592 113.9 0.7124 0.22 0.001202 0.01389
hsa-miR-9-5p 876.7 -0.6181 0.23 0.007207 0.04166
hsa-miR-93-3p 4.183 0.5067 0.2341 0.03042 0.112
hsa-miR-330-3p 14.43 -0.541 0.2075 0.00914 0.0478
hsa-miR-154-5p 3.18 -0.701 0.2524 0.005477 0.0347
hsa-miR-539-5p 1.734 -1.196 0.3564 0.0007895 0.01101
hsa-miR-421 87.94 -0.4284 0.1353 0.001543 0.01646
hsa-miR-138-1-3p 4.254 -1.418 0.3203 9.543e-06 0.0005947
hsa-miR-874-3p 100.7 -0.8509 0.2016 2.435e-05 0.00107
hsa-miR-744-3p 2.717 -0.9017 0.2596 0.0005141 0.008146
hsa-miR-184 18.71 -0.9876 0.2422 4.542e-05 0.001425
hsa-miR-376a-3p 3.282 -0.8949 0.2755 0.001163 0.01389
hsa-miR-221-3p 582.2 -0.2866 0.135 0.0337 0.1163
hsa-miR-219a-2-3p 322.6 -0.5995 0.2785 0.03136 0.1134
hsa-miR-25-3p 1006 0.3117 0.1435 0.02986 0.1114
hsa-miR-182-5p 242.6 0.6913 0.2999 0.02114 0.08548
hsa-miR-636 0.6453 1.056 0.4448 0.01759 0.07382
hsa-miR-128-1-5p 9.605 -0.9042 0.2756 0.001034 0.01318
hsa-miR-409-3p 128 -0.6981 0.2266 0.002062 0.01941
hsa-miR-758-5p 0.4859 -1.277 0.4134 0.002001 0.01911
hsa-miR-326 15.56 -0.7 0.2323 0.002584 0.02193
hsa-miR-369-3p 4.031 -0.9407 0.3302 0.004389 0.03013
hsa-miR-129-1-3p 3.177 -0.7264 0.3089 0.01871 0.07706
hsa-miR-664a-3p 75.36 0.6465 0.2559 0.01153 0.05508
hsa-miR-518b 2.998 0.761 0.3573 0.03316 0.1159
hsa-miR-3125 0.5497 -0.9539 0.3805 0.01219 0.05757
hsa-miR-4705 0.7427 -1.126 0.409 0.005899 0.03633
hsa-miR-127-3p 3613 -1.181 0.2499 2.307e-06 0.0002404
hsa-miR-199a-3p|hsa-miR-199b-3p 401.3 -0.6741 0.2244 0.002662 0.02193
hsa-miR-148a-3p 8096 0.544 0.173 0.001663 0.01712
hsa-miR-4685-3p 1.053 1.007 0.3483 0.00382 0.02736
hsa-miR-145-5p 35.06 -0.7679 0.2195 0.0004689 0.007725
hsa-miR-520d-5p 0.8816 1.134 0.3472 0.001093 0.01359
hsa-miR-329-3p 7.318 -0.959 0.2897 0.0009307 0.01227
hsa-miR-2114-5p 1.12 -0.766 0.3487 0.02806 0.1063
hsa-miR-3620-3p 0.5875 0.9881 0.3761 0.008604 0.04648
hsa-miR-132-3p 40.2 -0.8564 0.1801 1.974e-06 0.0002404
hsa-miR-1911-5p 2167 0.697 0.2079 0.0008021 0.01101
hsa-miR-191-5p 7269 0.4891 0.1545 0.001549 0.01646
hsa-miR-129-2-3p 21.29 -0.6975 0.2408 0.00377 0.02736
hsa-miR-524-3p 1.389 0.9829 0.346 0.004499 0.03029
hsa-miR-873-5p 27.98 -0.791 0.2295 0.0005682 0.008509
hsa-miR-708-5p 9.269 -0.9309 0.2859 0.001132 0.01381
hsa-miR-301a-3p 30 -0.4517 0.2176 0.03794 0.1263
hsa-miR-148b-5p 4.034 0.4832 0.2322 0.03742 0.1257
hsa-miR-767-3p 4.775 0.7008 0.2578 0.006558 0.03917
hsa-miR-212-3p 3.259 -1.414 0.2701 1.644e-07 3.611e-05
hsa-miR-101-5p 5.839 -0.8768 0.2015 1.356e-05 0.0006872
hsa-miR-151a-3p 2781 0.2392 0.115 0.03758 0.1257
hsa-miR-1247-3p 1.193 -0.7795 0.3635 0.03198 0.1142
hsa-miR-410-3p 110.5 -0.5745 0.2543 0.02385 0.09356
hsa-miR-194-5p 7.451 -0.5242 0.2131 0.01389 0.06315
hsa-miR-363-3p 340.8 0.3906 0.1563 0.01245 0.05778
hsa-miR-370-3p 12.54 -0.8046 0.3055 0.008435 0.04594
hsa-miR-136-5p 37.68 -0.9408 0.2179 1.583e-05 0.000745
hsa-miR-455-5p 4.511 -0.7606 0.2669 0.004379 0.03013
hsa-miR-889-3p 21.8 -0.5678 0.2763 0.03987 0.1314
hsa-miR-375 468 0.392 0.1844 0.03348 0.1161
hsa-miR-590-3p 1.423 -0.7598 0.3157 0.01611 0.07031
hsa-miR-338-3p 497.9 -0.5836 0.2383 0.01431 0.0643
hsa-miR-515-5p 1.737 0.9201 0.3725 0.0135 0.06176
hsa-miR-181c-5p 710.6 -0.4105 0.1517 0.006827 0.04017
hsa-miR-4707-3p 0.5709 -1.17 0.4006 0.003505 0.02595
hsa-miR-382-3p 3.293 -0.9755 0.2924 0.0008505 0.01144
hsa-miR-139-5p 24.86 -0.8967 0.2452 0.0002551 0.00467
hsa-miR-92a-3p 2150 0.5528 0.2096 0.008365 0.04594
hsa-miR-335-5p 230.5 -0.5058 0.1912 0.008165 0.04522
hsa-miR-134-5p 42.24 -0.7608 0.2443 0.001844 0.01813
hsa-miR-520a-3p 5.435 0.7554 0.3512 0.03149 0.1134
hsa-miR-1271-5p 7.173 -0.8382 0.3303 0.01116 0.05405
hsa-miR-6500-3p 1.094 -1.071 0.3106 0.000564 0.008509
hsa-miR-651-5p 2.969 -0.5739 0.2688 0.03272 0.1153
hsa-miR-124-5p 2.07 -0.9481 0.3667 0.00972 0.04948
hsa-miR-383-5p 17.18 -1.004 0.3218 0.001807 0.01804
hsa-miR-199a-5p 58.64 -0.712 0.2572 0.005638 0.03538
hsa-miR-193b-5p 5.804 -1.148 0.3039 0.0001589 0.003394
hsa-miR-190a-5p 10.82 0.6463 0.2399 0.007063 0.04119
hsa-miR-192-5p 904.5 -0.6435 0.1656 0.0001016 0.002575
hsa-miR-125a-3p 17.53 0.4555 0.2004 0.02301 0.09134
hsa-miR-1287-5p 6.571 -0.5291 0.2016 0.008681 0.04651
hsa-miR-181a-3p 54.87 -0.6971 0.1993 0.0004687 0.007725
hsa-miR-488-3p 8.993 -0.9106 0.2488 0.0002514 0.00467
hsa-miR-1912 95.33 0.4131 0.1852 0.02569 0.09902
hsa-miR-181d-5p 104.8 -0.4356 0.1803 0.01565 0.06878
hsa-miR-320a 2467 -0.5025 0.1933 0.009327 0.0484
hsa-miR-323b-3p 27.61 -0.758 0.25 0.002429 0.02186
hsa-miR-3663-3p 0.4704 -1.473 0.4061 0.0002858 0.005091
hsa-miR-9-3p 55.52 -0.9972 0.2152 3.6e-06 0.0002965
hsa-miR-218-5p 51.33 -0.732 0.1985 0.0002261 0.004656
hsa-miR-769-5p 1087 -0.8644 0.2189 7.855e-05 0.002251
hsa-miR-493-3p 1.488 -0.9126 0.3216 0.004551 0.03029
hsa-miR-770-5p 1.179 -1.733 0.3684 2.553e-06 0.0002404
hsa-miR-199b-5p 5.614 -1.433 0.2902 7.902e-07 0.0001302
hsa-miR-3117-3p 0.707 -1.463 0.3583 4.466e-05 0.001425
hsa-miR-539-3p 1.868 -0.7016 0.3367 0.03716 0.1256
hsa-miR-92b-3p 1898 0.5357 0.2506 0.03256 0.1153
hsa-miR-30c-5p 1094 0.5092 0.1833 0.005468 0.0347
hsa-miR-548ab 0.9996 -1.077 0.3563 0.002508 0.02186
hsa-miR-30c-2-3p 98.38 0.6701 0.1764 0.0001452 0.0033
hsa-miR-219a-5p 99.4 -0.9702 0.3078 0.001624 0.01699
hsa-miR-20a-5p 9.595 -0.6621 0.3088 0.03205 0.1142
hsa-miR-1224-5p 2.667 -1.2 0.35 0.0006059 0.00872
hsa-miR-33a-5p 2.434 -0.7783 0.2586 0.002619 0.02193
hsa-let-7e-5p 658 0.4762 0.1657 0.004059 0.02865
hsa-miR-935 1.511 -0.7691 0.3543 0.02992 0.1114
hsa-miR-758-3p 2.115 -0.9889 0.327 0.002496 0.02186
hsa-miR-138-2-3p 0.9391 -1.136 0.356 0.001425 0.01592
hsa-miR-598-3p 29.59 -1.009 0.2447 3.702e-05 0.001355
hsa-miR-223-3p 25.94 -0.5967 0.2524 0.01809 0.07544
hsa-miR-4662a-5p 1.26 0.8031 0.337 0.01716 0.07294
hsa-miR-323a-5p 2.499 -0.9685 0.3792 0.01065 0.05197
hsa-miR-582-5p 1.671 -0.9203 0.3519 0.008917 0.04739
hsa-miR-2467-5p 1.968 -0.8235 0.2984 0.005787 0.03598
hsa-miR-129-5p 223.9 -0.8943 0.2434 0.0002386 0.00467

Understanding Your Results

The table above displays differentially expressed miRNAs for selected Atlas data.
  • The Checkbox column allows you to select a given miRNA for further downstream analysis.
    You can click the checkbox in the upper left corner of the table to select all visible miRNAs.
  • The Identifiers column contains all of your miRNA identifiers.
  • The Base Mean column contains "the average of the normalized count values, divided by the size factors, taken over all samples [in the original dataset]" for each miRNA.[1]
  • The log2 Fold Change column contains the "effect size estimate" for each miRNA.[1]
  • The Standard Error column contains the "standard error estimate for the log2 fold change estimate" for each miRNA.[1]
  • The p-value column contains the Wald test p-value for each miRNA.[1]
  • The Adjusted p-value column contains the Benjamini-Hochberg adjusted p-value for each miRNA.[1]
By default, the table is sorted by adjusted p-value, but you can sort by any of the columns.

Downstream Analysis

When you have selected your miRNAs of interest (via the checkboxes on the left side of the table),
you can perform downstream analyses by clicking the "Analyze Selected miRNAs" button above the table.

See descriptions of all available downstream analysis tools below.

Pathway Finder
  • Use Pathway Finder (hosted by WikiPathways) to find pathways containing miRNAs of interest (or protein targets of those miRNAs).
  • Currently, the top ten differentially expressed miRNAs (via DESeq2) are used for analysis.
  • Click a given pathway title to visualize its contents at the bottom of the page.
  • Then, select a given miRNA to highlight its associated target(s).
  • The pathway visualization is interactive - zoom in or out by using the + and - icons, and click a given gene product to learn more about it.
  • Designed and implemented by Kristina Hanspers, Anders Riutta, and Alexander Pico at the Gladstone Institutes, San Francisco, CA.
  • Integrated into the exRNA Atlas by William Thistlethwaite and Neethu Shah at the Bioinformatics Research Lab, Baylor College of Medicine, Houston, TX.

References

[1] Love, M. I., Anders, S., Kim V., & Huber W. (2017, Aug 9). RNA-seq workflow: gene-level exploratory analysis and differential expression. Retrieved from http://www.bioconductor.org/help/workflows/rnaseqGene/

DESeq2 designed and implemented by Michael Love, Simon Anders, and Wolfgang Huber (PubMed).
DESeq2 integrated into the exRNA Atlas by William Thistlethwaite and Neethu Shah at the Bioinformatics Research Lab, Baylor College of Medicine, Houston, TX.