Coexpression cluster:C2530: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
| (3 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
{ | |||
Latest revision as of 12:07, 17 September 2013
Full id: C2530_Retinal_Mallassezderived_Bronchial_Keratinocyte_small_Hep2_Tracheal
Phase1 CAGE Peaks
| Hg19::chr1:155278605..155278621,+ | p2@FDPS |
| Hg19::chr1:155278625..155278745,+ | p1@FDPS |
| Hg19::chr8:11660227..11660306,+ | p1@FDFT1 |
| Hg19::chrX:151999599..151999615,+ | p1@NSDHL |
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 1.25863435561633e-06 | 0.000265571849035045 | 2 | 19 | Steroid biosynthesis (KEGG):00100 |
| 6.31961929821581e-05 | 0.0100007975394265 | 3 | 1138 | Metabolic pathways (KEGG):01100 |
| 1.17374162251993e-10 | 7.42978447055117e-08 | 3 | 15 | Cholesterol Biosynthesis (Wikipathways):WP1795 |
| 1.02702753121762e-06 | 0.000265571849035045 | 3 | 289 | Metabolism of lipids and lipoproteins (Reactome):REACT_22258 |
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0006695 | cholesterol biosynthetic process | 2.35846206673679e-08 |
| GO:0016126 | sterol biosynthetic process | 2.7973410948078e-08 |
| GO:0008203 | cholesterol metabolic process | 2.60032406071113e-07 |
| GO:0006694 | steroid biosynthetic process | 2.7490233849884e-07 |
| GO:0016125 | sterol metabolic process | 2.7490233849884e-07 |
| GO:0008202 | steroid metabolic process | 3.11636752412651e-06 |
| GO:0008610 | lipid biosynthetic process | 8.93433186074538e-06 |
| GO:0004659 | prenyltransferase activity | 9.14037355238191e-06 |
| GO:0006066 | alcohol metabolic process | 1.66208797318529e-05 |
| GO:0008299 | isoprenoid biosynthetic process | 1.95292984653651e-05 |
| GO:0006720 | isoprenoid metabolic process | 3.13236575847922e-05 |
| GO:0044255 | cellular lipid metabolic process | 6.42619524810821e-05 |
| GO:0016765 | transferase activity, transferring alkyl or aryl (other than methyl) groups | 9.10383300825682e-05 |
| GO:0006629 | lipid metabolic process | 0.000103018853577011 |
| GO:0004310 | farnesyl-diphosphate farnesyltransferase activity | 0.000369789826916284 |
| GO:0047012 | sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity | 0.000369789826916284 |
| GO:0004337 | geranyltranstransferase activity | 0.000657384784818225 |
| GO:0004161 | dimethylallyltranstransferase activity | 0.000657384784818225 |
| GO:0004311 | farnesyltranstransferase activity | 0.00124549783979476 |
| GO:0009058 | biosynthetic process | 0.00126128254597198 |
| GO:0003854 | 3-beta-hydroxy-delta5-steroid dehydrogenase activity | 0.00309827870602796 |
| GO:0022404 | molting cycle process | 0.00409408397409858 |
| GO:0001942 | hair follicle development | 0.00409408397409858 |
| GO:0042633 | hair cycle | 0.00409408397409858 |
| GO:0042303 | molting cycle | 0.00409408397409858 |
| GO:0022405 | hair cycle process | 0.00409408397409858 |
| GO:0005783 | endoplasmic reticulum | 0.00519523953746089 |
| GO:0016229 | steroid dehydrogenase activity | 0.0067557024387043 |
| GO:0016491 | oxidoreductase activity | 0.0140882656807064 |
| GO:0005737 | cytoplasm | 0.0238510504393937 |
| GO:0008544 | epidermis development | 0.0256644984393836 |
| GO:0007398 | ectoderm development | 0.0268795976235625 |
| GO:0016616 | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | 0.0274868037710153 |
| GO:0016614 | oxidoreductase activity, acting on CH-OH group of donors | 0.0285746974756521 |
| GO:0016740 | transferase activity | 0.049679821594233 |
| GO:0009888 | tissue development | 0.049679821594233 |
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| animal cell | 5.00e-23 | 679 |
| eukaryotic cell | 5.00e-23 | 679 |
| embryonic cell | 4.11e-19 | 250 |
| somatic cell | 1.47e-17 | 588 |
| epithelial cell | 1.01e-14 | 253 |
| native cell | 2.42e-14 | 722 |
| mesodermal cell | 1.32e-11 | 121 |
| contractile cell | 6.89e-09 | 59 |
| electrically responsive cell | 8.04e-08 | 61 |
| electrically active cell | 8.04e-08 | 61 |
| muscle precursor cell | 9.97e-08 | 58 |
| myoblast | 9.97e-08 | 58 |
| multi-potent skeletal muscle stem cell | 9.97e-08 | 58 |
| muscle cell | 1.03e-07 | 55 |
| non-terminally differentiated cell | 3.53e-07 | 106 |
| ectodermal cell | 7.43e-07 | 72 |
| Ontology term | p-value | n |
|---|---|---|
| cell layer | 7.93e-16 | 309 |
| epithelium | 5.58e-15 | 306 |
| organism subdivision | 9.81e-13 | 264 |
| unilaminar epithelium | 3.25e-12 | 148 |
| multi-tissue structure | 7.25e-11 | 342 |
| anatomical cluster | 2.57e-10 | 373 |
| multilaminar epithelium | 4.39e-10 | 83 |
| trunk mesenchyme | 5.91e-10 | 122 |
| epithelial vesicle | 7.91e-10 | 78 |
| mesenchyme | 2.46e-09 | 160 |
| entire embryonic mesenchyme | 2.46e-09 | 160 |
| trunk | 5.61e-09 | 199 |
| epithelial tube | 6.46e-09 | 117 |
| ectodermal placode | 1.15e-08 | 31 |
| somite | 1.99e-08 | 71 |
| presomitic mesoderm | 1.99e-08 | 71 |
| presumptive segmental plate | 1.99e-08 | 71 |
| dermomyotome | 1.99e-08 | 71 |
| trunk paraxial mesoderm | 1.99e-08 | 71 |
| vasculature | 2.09e-08 | 78 |
| vascular system | 2.09e-08 | 78 |
| paraxial mesoderm | 2.64e-08 | 72 |
| presumptive paraxial mesoderm | 2.64e-08 | 72 |
| dense mesenchyme tissue | 5.94e-08 | 73 |
| larynx | 1.23e-07 | 9 |
| primordium | 1.97e-07 | 160 |
| organ part | 5.51e-07 | 218 |
Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
| MA0003.1 | 0.443649 |
| MA0004.1 | 0.71247 |
| MA0006.1 | 1.31813 |
| MA0007.1 | 0.6918 |
| MA0009.1 | 1.20602 |
| MA0014.1 | 0.524262 |
| MA0017.1 | 0.577281 |
| MA0019.1 | 0.873355 |
| MA0024.1 | 1.09684 |
| MA0025.1 | 1.34373 |
| MA0027.1 | 2.83281 |
| MA0028.1 | 1.35734 |
| MA0029.1 | 1.11704 |
| MA0030.1 | 1.10506 |
| MA0031.1 | 1.03735 |
| MA0038.1 | 1.92746 |
| MA0040.1 | 1.12314 |
| MA0041.1 | 0.732902 |
| MA0042.1 | 0.697662 |
| MA0043.1 | 1.20635 |
| MA0046.1 | 1.19471 |
| MA0048.1 | 0.25531 |
| MA0050.1 | 0.69864 |
| MA0051.1 | 0.820063 |
| MA0052.1 | 1.12718 |
| MA0055.1 | 0.125954 |
| MA0056.1 | 0 |
| MA0057.1 | 0.248209 |
| MA0058.1 | 0.605914 |
| MA0059.1 | 0.604454 |
| MA0060.1 | 9.62028 |
| MA0061.1 | 0.946082 |
| MA0063.1 | 0 |
| MA0066.1 | 0.825101 |
| MA0067.1 | 1.53181 |
| MA0068.1 | 0.313194 |
| MA0069.1 | 1.19071 |
| MA0070.1 | 1.17908 |
| MA0071.1 | 0.782546 |
| MA0072.1 | 1.1744 |
| MA0073.1 | 0.00636811 |
| MA0074.1 | 1.91637 |
| MA0076.1 | 1.51122 |
| MA0077.1 | 1.16637 |
| MA0078.1 | 0.926725 |
| MA0081.1 | 0.604638 |
| MA0083.1 | 1.21381 |
| MA0084.1 | 1.72172 |
| MA0087.1 | 1.17185 |
| MA0088.1 | 0.536981 |
| MA0089.1 | 0 |
| MA0090.1 | 0.640115 |
| MA0091.1 | 0.715356 |
| MA0092.1 | 0.673508 |
| MA0093.1 | 0.535768 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.83965 |
| MA0101.1 | 1.33363 |
| MA0103.1 | 0.521546 |
| MA0105.1 | 0.656404 |
| MA0106.1 | 0.869173 |
| MA0107.1 | 0.453492 |
| MA0108.2 | 1.03412 |
| MA0109.1 | 0 |
| MA0111.1 | 0.655276 |
| MA0113.1 | 0.886811 |
| MA0114.1 | 0.447443 |
| MA0115.1 | 1.45393 |
| MA0116.1 | 0.457606 |
| MA0117.1 | 1.24497 |
| MA0119.1 | 0.586221 |
| MA0122.1 | 1.27173 |
| MA0124.1 | 1.41151 |
| MA0125.1 | 1.32534 |
| MA0130.1 | 0 |
| MA0131.1 | 0.94608 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.23748 |
| MA0136.1 | 0.832277 |
| MA0139.1 | 0.344952 |
| MA0140.1 | 1.83481 |
| MA0141.1 | 0.602484 |
| MA0142.1 | 1.00381 |
| MA0143.1 | 0.887001 |
| MA0144.1 | 0.430413 |
| MA0145.1 | 0.569905 |
| MA0146.1 | 0.8309 |
| MA0147.1 | 0.46175 |
| MA0148.1 | 0.739888 |
| MA0149.1 | 0.769072 |
| MA0062.2 | 0.931615 |
| MA0035.2 | 1.83323 |
| MA0039.2 | 0.483275 |
| MA0138.2 | 0.928035 |
| MA0002.2 | 1.75253 |
| MA0137.2 | 0.558189 |
| MA0104.2 | 1.01696 |
| MA0047.2 | 0.856092 |
| MA0112.2 | 0.187982 |
| MA0065.2 | 0.199162 |
| MA0150.1 | 0.633493 |
| MA0151.1 | 0 |
| MA0152.1 | 0.78681 |
| MA0153.1 | 1.30799 |
| MA0154.1 | 0.229241 |
| MA0155.1 | 0.180766 |
| MA0156.1 | 0.560797 |
| MA0157.1 | 0.97481 |
| MA0158.1 | 0 |
| MA0159.1 | 0.462502 |
| MA0160.1 | 1.78721 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0928415 |
| MA0163.1 | 0.253219 |
| MA0164.1 | 0.90014 |
| MA0080.2 | 0.535868 |
| MA0018.2 | 0.870662 |
| MA0099.2 | 0.7872 |
| MA0079.2 | 0.0626799 |
| MA0102.2 | 1.75932 |
| MA0258.1 | 0.418966 |
| MA0259.1 | 0.471671 |
| MA0442.1 | 0 |
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
| TF | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| ATF3#467 | 2 | 11.2315872630044 | 0.0111955903992222 | 0.0411289973514498 |
| BRCA1#672 | 3 | 15.1381729824178 | 0.000468218442143119 | 0.00430195002014474 |
| CCNT2#905 | 4 | 6.33620157696263 | 0.000620310058721564 | 0.00512292916517646 |
| CEBPB#1051 | 3 | 5.97836071936861 | 0.00715383248472697 | 0.0297297803856751 |
| CHD2#1106 | 4 | 10.3440228341169 | 8.73193255208051e-05 | 0.00129098853879776 |
| ELF1#1997 | 4 | 4.25809795880754 | 0.00304152556578124 | 0.016094334932595 |
| EP300#2033 | 3 | 5.0804562946674 | 0.0114429840539824 | 0.0418963649996097 |
| ESR1#2099 | 2 | 15.3843016480772 | 0.00606557262969351 | 0.0268401974354953 |
| ETS1#2113 | 4 | 9.72876092220234 | 0.000111595531741814 | 0.00154595115261749 |
| FOS#2353 | 4 | 8.9979553088944 | 0.000152514771116863 | 0.00194939299726766 |
| FOSL2#2355 | 4 | 16.9302006045617 | 1.2165416097647e-05 | 0.000304030603451102 |
| GATA1#2623 | 3 | 10.1702311078503 | 0.00151515816849827 | 0.00966419958225181 |
| GATA2#2624 | 3 | 9.5586988001655 | 0.00181815161835744 | 0.0109004556182338 |
| GATA3#2625 | 2 | 13.618258178603 | 0.0076966520809334 | 0.0316930428845406 |
| GTF2F1#2962 | 3 | 9.55474565756824 | 0.00182036231930478 | 0.010899943829026 |
| HEY1#23462 | 4 | 4.04011104310571 | 0.0037530463691798 | 0.0186153310101999 |
| HMGN3#9324 | 3 | 6.13391079251294 | 0.00664069668332472 | 0.0282976751768636 |
| IRF1#3659 | 4 | 7.6371637535639 | 0.000293885399618549 | 0.00307607709468447 |
| IRF3#3661 | 3 | 35.2364641586172 | 3.79279212646878e-05 | 0.000719817221327045 |
| MAX#4149 | 3 | 4.83941663175534 | 0.0131573713783684 | 0.0466253633749122 |
| MXI1#4601 | 4 | 9.9615716287593 | 0.000101522475495045 | 0.00142416464986259 |
| NFYA#4800 | 4 | 18.4255806998305 | 8.67100748407158e-06 | 0.000234426961074023 |
| NFYB#4801 | 4 | 16.7597932535365 | 1.26678572070404e-05 | 0.00031137169659828 |
| NR2C2#7182 | 2 | 16.3073054526204 | 0.00541182534464822 | 0.0245570745207558 |
| PBX3#5090 | 2 | 10.9572563433721 | 0.0117453018068803 | 0.0428455317991189 |
| REST#5978 | 3 | 7.23752153709602 | 0.00410469730419261 | 0.0195802723007478 |
| RFX5#5993 | 4 | 12.0479108271951 | 4.74457429336527e-05 | 0.000826966946970586 |
| SIN3A#25942 | 4 | 5.40888472681514 | 0.00116817238488516 | 0.00796674648720261 |
| SP1#6667 | 4 | 5.6983813781409 | 0.000948260606533398 | 0.00684513336229897 |
| SP2#6668 | 2 | 13.0767652469223 | 0.00833003653661494 | 0.0328096502431561 |
| SREBF1#6720 | 4 | 47.0058494404883 | 2.04523668136926e-07 | 1.10331856283845e-05 |
| SREBF2#6721 | 4 | 436.943262411348 | 2.70480926640298e-11 | 3.17758801995344e-09 |
| STAT1#6772 | 2 | 10.3532937485996 | 0.0131077747617126 | 0.0464922020152319 |
| TAF1#6872 | 4 | 3.34304628574529 | 0.00800566489870165 | 0.0322371852388765 |
| TAF7#6879 | 3 | 8.57480205369294 | 0.0025005543351524 | 0.014034576215014 |
| TAL1#6886 | 2 | 14.9343083387201 | 0.00642807757788807 | 0.0279481284774594 |
| TBP#6908 | 4 | 3.70677068709639 | 0.00529637781478435 | 0.0244334291531544 |
| TCF7L2#6934 | 3 | 8.07763242235301 | 0.00297838168583462 | 0.0158647016314011 |
| THAP1#55145 | 2 | 15.6845723014257 | 0.00584046967835792 | 0.0262489376339626 |
| USF1#7391 | 3 | 4.77112445790597 | 0.0137046588718802 | 0.048305800469804 |
| USF2#7392 | 3 | 9.7441480388022 | 0.00171834184841007 | 0.0107205438653584 |
| ZBTB33#10009 | 3 | 23.7485437724859 | 0.000122945190881838 | 0.0016555276934642 |
| ZNF143#7702 | 3 | 10.1256574141709 | 0.00153486161068818 | 0.00976839803526285 |
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
This analysis result is provided for C0 - C305 clusters.
