Coexpression cluster:C747
From FANTOM5_SSTAR
Full id: C747_Mesenchymal_alveolar_Trabecular_Alveolar_carcinoid_Renal_chronic
Phase1 CAGE Peaks
Hg19::chr12:2986206..2986258,- | p2@FOXM1 |
Hg19::chr12:6960407..6960464,- | p1@CDCA3 |
Hg19::chr16:23690138..23690158,+ | p3@PLK1 |
Hg19::chr16:23690160..23690176,+ | p2@PLK1 |
Hg19::chr16:23690184..23690267,+ | p1@PLK1 |
Hg19::chr17:76210318..76210366,+ | p1@BIRC5 |
Hg19::chr17:76210367..76210385,+ | p2@BIRC5 |
Hg19::chr17:76220151..76220166,+ | p@chr17:76220151..76220166 + |
Hg19::chr20:44441304..44441319,+ | p2@UBE2C |
Hg19::chr3:52188397..52188450,- | p1@POC1A |
Hg19::chr9:91926103..91926119,+ | p1@CKS2 |
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 |
---|---|---|---|---|
2.59719623007301e-05 | 0.00822012606818106 | 3 | 315 | Cell Cycle, Mitotic (Reactome):REACT_152 |
3.12165196450452e-07 | 0.000197600569353136 | 4 | 346 | {CDC2,351} (Static Module):NA |
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:0000279 | M phase | 6.90478736690457e-08 |
GO:0022403 | cell cycle phase | 8.83920725918899e-08 |
GO:0022402 | cell cycle process | 8.25432434157677e-07 |
GO:0007067 | mitosis | 1.31800666603262e-06 |
GO:0000087 | M phase of mitotic cell cycle | 1.31800666603262e-06 |
GO:0051301 | cell division | 1.31800666603262e-06 |
GO:0007049 | cell cycle | 1.54018451911913e-06 |
GO:0000278 | mitotic cell cycle | 3.10586241182863e-06 |
GO:0031536 | positive regulation of exit from mitosis | 3.50012641760176e-06 |
GO:0010458 | exit from mitosis | 3.72023214421962e-05 |
GO:0007096 | regulation of exit from mitosis | 3.72023214421962e-05 |
GO:0007051 | spindle organization and biogenesis | 7.47271452394409e-05 |
GO:0000074 | regulation of progression through cell cycle | 0.000329835940259241 |
GO:0051726 | regulation of cell cycle | 0.000329835940259241 |
GO:0007088 | regulation of mitosis | 0.000770058464162874 |
GO:0000226 | microtubule cytoskeleton organization and biogenesis | 0.00167727124825463 |
GO:0031021 | interphase microtubule organizing center | 0.00209861408357055 |
GO:0048015 | phosphoinositide-mediated signaling | 0.00225905088143288 |
GO:0005813 | centrosome | 0.00225905088143288 |
GO:0005815 | microtubule organizing center | 0.00278551449326256 |
GO:0008054 | cyclin catabolic process | 0.00339750608701829 |
GO:0031503 | protein complex localization | 0.00486425299265298 |
GO:0045931 | positive regulation of progression through mitotic cell cycle | 0.00766592103107661 |
GO:0019932 | second-messenger-mediated signaling | 0.00766592103107661 |
GO:0050000 | chromosome localization | 0.00792518087701449 |
GO:0043027 | caspase inhibitor activity | 0.00792518087701449 |
GO:0051303 | establishment of chromosome localization | 0.00792518087701449 |
GO:0031577 | spindle checkpoint | 0.00844579235707201 |
GO:0005814 | centriole | 0.00844579235707201 |
GO:0007017 | microtubule-based process | 0.00844579235707201 |
GO:0030496 | midbody | 0.00891451629983814 |
GO:0005881 | cytoplasmic microtubule | 0.00891451629983814 |
GO:0043154 | negative regulation of caspase activity | 0.00972421121857813 |
GO:0016538 | cyclin-dependent protein kinase regulator activity | 0.0115338861723623 |
GO:0000086 | G2/M transition of mitotic cell cycle | 0.0173081643590862 |
GO:0005876 | spindle microtubule | 0.0178159169112155 |
GO:0015630 | microtubule cytoskeleton | 0.0181776697464586 |
GO:0043028 | caspase regulator activity | 0.0193994720605775 |
GO:0006512 | ubiquitin cycle | 0.0193994720605775 |
GO:0043161 | proteasomal ubiquitin-dependent protein catabolic process | 0.0195054927304112 |
GO:0044450 | microtubule organizing center part | 0.0195054927304112 |
GO:0051656 | establishment of organelle localization | 0.0195054927304112 |
GO:0045787 | positive regulation of progression through cell cycle | 0.0198787562119038 |
GO:0050790 | regulation of catalytic activity | 0.0207930693452798 |
GO:0043687 | post-translational protein modification | 0.0219524760693981 |
GO:0065009 | regulation of a molecular function | 0.0234910667351854 |
GO:0007346 | regulation of progression through mitotic cell cycle | 0.0234910667351854 |
GO:0007010 | cytoskeleton organization and biogenesis | 0.0234910667351854 |
GO:0051640 | organelle localization | 0.0234910667351854 |
GO:0007127 | meiosis I | 0.0234910667351854 |
GO:0000910 | cytokinesis | 0.023726604291929 |
GO:0008283 | cell proliferation | 0.026393228548436 |
GO:0004869 | cysteine protease inhibitor activity | 0.0275176371779979 |
GO:0006464 | protein modification process | 0.031106816416925 |
GO:0000079 | regulation of cyclin-dependent protein kinase activity | 0.031106816416925 |
GO:0008017 | microtubule binding | 0.031106816416925 |
GO:0050794 | regulation of cellular process | 0.0316698104268787 |
GO:0043412 | biopolymer modification | 0.0326941435235869 |
GO:0000075 | cell cycle checkpoint | 0.0337256129752269 |
GO:0044430 | cytoskeletal part | 0.0342664867856905 |
GO:0043281 | regulation of caspase activity | 0.0349395606960469 |
GO:0050789 | regulation of biological process | 0.0376828890740395 |
GO:0015631 | tubulin binding | 0.0376828890740395 |
GO:0051327 | M phase of meiotic cell cycle | 0.0376828890740395 |
GO:0007126 | meiosis | 0.0376828890740395 |
GO:0051321 | meiotic cell cycle | 0.0381820259946129 |
GO:0016567 | protein ubiquitination | 0.0386659523883696 |
GO:0000775 | chromosome, pericentric region | 0.0395291491514415 |
GO:0032446 | protein modification by small protein conjugation | 0.0395291491514415 |
GO:0005819 | spindle | 0.0395291491514415 |
GO:0016043 | cellular component organization and biogenesis | 0.0407942602760004 |
GO:0051329 | interphase of mitotic cell cycle | 0.0418585026518499 |
GO:0051325 | interphase | 0.0436975580360055 |
GO:0065007 | biological regulation | 0.0447251946760065 |
GO:0019887 | protein kinase regulator activity | 0.0489140954037165 |
GO:0046982 | protein heterodimerization activity | 0.0489140954037165 |
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>disease_data<br>
Ontology term | p-value | n |
---|---|---|
animal cell | 3.90e-26 | 679 |
eukaryotic cell | 3.90e-26 | 679 |
epithelial cell | 4.56e-23 | 253 |
embryonic cell | 4.27e-16 | 250 |
native cell | 2.15e-14 | 722 |
migratory neural crest cell | 4.78e-09 | 41 |
neurectodermal cell | 2.76e-08 | 59 |
mesodermal cell | 2.51e-07 | 121 |
squamous epithelial cell | 2.64e-07 | 63 |
epithelial cell of nephron | 3.93e-07 | 15 |
kidney cell | 4.13e-07 | 17 |
kidney epithelial cell | 4.13e-07 | 17 |
ectodermal cell | 5.19e-07 | 72 |
lining cell | 6.78e-07 | 58 |
barrier cell | 6.78e-07 | 58 |
non-terminally differentiated cell | 8.04e-07 | 106 |
neural cell | 9.53e-07 | 25 |
Ontology term | p-value | n |
---|---|---|
nephron epithelium | 3.93e-07 | 15 |
renal tubule | 3.93e-07 | 15 |
nephron tubule | 3.93e-07 | 15 |
nephron | 3.93e-07 | 15 |
uriniferous tubule | 3.93e-07 | 15 |
nephrogenic mesenchyme | 3.93e-07 | 15 |
Ontology term | p-value | n |
---|---|---|
cancer | 8.91e-38 | 235 |
disease of cellular proliferation | 7.43e-37 | 239 |
cell type cancer | 1.44e-18 | 143 |
organ system cancer | 4.43e-17 | 137 |
hematologic cancer | 7.70e-15 | 51 |
immune system cancer | 7.70e-15 | 51 |
carcinoma | 1.26e-14 | 106 |
leukemia | 6.23e-11 | 39 |
myeloid leukemia | 1.21e-07 | 31 |
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 | 2.25715 |
MA0004.1 | 1.64978 |
MA0006.1 | 0.605586 |
MA0007.1 | 0.885261 |
MA0009.1 | 0.79061 |
MA0014.1 | 2.1035 |
MA0017.1 | 0.24363 |
MA0019.1 | 0.486183 |
MA0024.1 | 0.688373 |
MA0025.1 | 2.12648 |
MA0027.1 | 2.39404 |
MA0028.1 | 0.224112 |
MA0029.1 | 0.707146 |
MA0030.1 | 0.696006 |
MA0031.1 | 0.633489 |
MA0038.1 | 1.97347 |
MA0040.1 | 0.712837 |
MA0041.1 | 0.366339 |
MA0042.1 | 0.337481 |
MA0043.1 | 0.790919 |
MA0046.1 | 0.779945 |
MA0048.1 | 1.12059 |
MA0050.1 | 1.61016 |
MA0051.1 | 0.439895 |
MA0052.1 | 0.716602 |
MA0055.1 | 0.736537 |
MA0056.1 | 0 |
MA0057.1 | 0.0465155 |
MA0058.1 | 2.8909 |
MA0059.1 | 1.34253 |
MA0060.1 | 6.47493 |
MA0061.1 | 0.330174 |
MA0063.1 | 0 |
MA0066.1 | 0.444231 |
MA0067.1 | 1.1037 |
MA0068.1 | 0.0758327 |
MA0069.1 | 0.776171 |
MA0070.1 | 0.765217 |
MA0071.1 | 0.40788 |
MA0072.1 | 0.760818 |
MA0073.1 | 0.00132306 |
MA0074.1 | 1.11883 |
MA0076.1 | 0.278993 |
MA0077.1 | 0.753278 |
MA0078.1 | 0.533387 |
MA0081.1 | 0.26424 |
MA0083.1 | 0.79797 |
MA0084.1 | 1.28962 |
MA0087.1 | 0.758426 |
MA0088.1 | 2.47064 |
MA0089.1 | 0 |
MA0090.1 | 0.792817 |
MA0091.1 | 0.351901 |
MA0092.1 | 0.318032 |
MA0093.1 | 2.53685 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 2.01706 |
MA0101.1 | 0.617985 |
MA0103.1 | 0.203171 |
MA0105.1 | 0.360248 |
MA0106.1 | 0.482519 |
MA0107.1 | 0.156959 |
MA0108.2 | 0.630531 |
MA0109.1 | 0 |
MA0111.1 | 0.303543 |
MA0113.1 | 0.498009 |
MA0114.1 | 0.153042 |
MA0115.1 | 1.02805 |
MA0116.1 | 0.935607 |
MA0117.1 | 0.827487 |
MA0119.1 | 0.698186 |
MA0122.1 | 0.852927 |
MA0124.1 | 0.98702 |
MA0125.1 | 0.904129 |
MA0130.1 | 0 |
MA0131.1 | 2.32762 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.820382 |
MA0136.1 | 0.450422 |
MA0139.1 | 0.637178 |
MA0140.1 | 1.04551 |
MA0141.1 | 0.2626 |
MA0142.1 | 0.602852 |
MA0143.1 | 0.498176 |
MA0144.1 | 2.00452 |
MA0145.1 | 1.62175 |
MA0146.1 | 0.700193 |
MA0147.1 | 1.51125 |
MA0148.1 | 0.372124 |
MA0149.1 | 0.396509 |
MA0062.2 | 0.320507 |
MA0035.2 | 0.404774 |
MA0039.2 | 0.556508 |
MA0138.2 | 1.323 |
MA0002.2 | 0.111226 |
MA0137.2 | 1.21272 |
MA0104.2 | 2.45237 |
MA0047.2 | 0.47109 |
MA0112.2 | 0.106997 |
MA0065.2 | 0.11899 |
MA0150.1 | 0.286461 |
MA0151.1 | 0 |
MA0152.1 | 0.411494 |
MA0153.1 | 0.887528 |
MA0154.1 | 0.353037 |
MA0155.1 | 0.462858 |
MA0156.1 | 0.231442 |
MA0157.1 | 0.576556 |
MA0158.1 | 0 |
MA0159.1 | 0.489747 |
MA0160.1 | 0.386031 |
MA0161.1 | 0 |
MA0162.1 | 0.178494 |
MA0163.1 | 0.585549 |
MA0164.1 | 0.509774 |
MA0080.2 | 0.21336 |
MA0018.2 | 0.483823 |
MA0099.2 | 0.411824 |
MA0079.2 | 0.239 |
MA0102.2 | 1.32663 |
MA0258.1 | 0.135061 |
MA0259.1 | 1.54967 |
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 | 3 | 6.12632032527511 | 0.0111162339916476 | 0.0408820466882767 |
BCLAF1#9774 | 3 | 5.90526753003323 | 0.0122864557732326 | 0.0445303010306995 |
CHD2#1106 | 7 | 6.58255998534709 | 1.82852745688608e-05 | 0.000416055727820751 |
E2F1#1869 | 10 | 4.46126292261757 | 1.10540139252827e-06 | 4.58123079501033e-05 |
E2F4#1874 | 10 | 11.5164184684404 | 9.56616236582045e-11 | 1.03854514690636e-08 |
E2F6#1876 | 9 | 4.1049455986615 | 1.83835844928222e-05 | 0.000418201520550175 |
EBF1#1879 | 7 | 5.66775162963482 | 4.91015352587259e-05 | 0.000852129485025934 |
ELF1#1997 | 8 | 3.09679851549639 | 0.000758011352761729 | 0.00595770226302545 |
ETS1#2113 | 7 | 6.19102967776512 | 2.74425924207753e-05 | 0.000583722384894777 |
FOSL2#2355 | 4 | 6.15643658347698 | 0.00286737656398896 | 0.015536494991774 |
HDAC2#3066 | 6 | 7.31761103815978 | 5.69712326977083e-05 | 0.000950482199954626 |
HEY1#23462 | 10 | 3.67282822100519 | 7.3527784911531e-06 | 0.000211140179498911 |
HNF4A#3172 | 6 | 12.6176129252475 | 2.49318000901648e-06 | 8.78492668561648e-05 |
HNF4G#3174 | 3 | 7.84184250721276 | 0.00562367765123593 | 0.0254211941749234 |
IRF1#3659 | 5 | 3.47143806980177 | 0.00894716207586585 | 0.0339324809369364 |
IRF3#3661 | 3 | 12.8132596940426 | 0.00139865858349401 | 0.00909951434632351 |
MAX#4149 | 9 | 5.27936359827855 | 2.09889244785612e-06 | 7.65652212230686e-05 |
MXI1#4601 | 8 | 7.2447793663704 | 1.28440155682788e-06 | 5.13166083372406e-05 |
MYC#4609 | 9 | 4.27277607677133 | 1.30375226575527e-05 | 0.000318732637835241 |
NFYA#4800 | 6 | 10.0503167453621 | 9.29686132166058e-06 | 0.000247566267101711 |
NFYB#4801 | 7 | 10.6653229795232 | 7.15961572771292e-07 | 3.20369797337879e-05 |
NRF1#4899 | 4 | 4.44010161734942 | 0.00927703375725097 | 0.0350460872666402 |
PBX3#5090 | 5 | 9.96114213033824 | 7.24136591048148e-05 | 0.00113863446902255 |
POLR2A#5430 | 10 | 1.95223016050734 | 0.0030407318184143 | 0.0161342778226577 |
POU2F2#5452 | 8 | 6.6226356783582 | 2.56270583551105e-06 | 9.01166446986324e-05 |
SIN3A#25942 | 10 | 4.9171679334683 | 4.26535327044908e-07 | 2.04907649591735e-05 |
SP1#6667 | 10 | 5.18034670740082 | 2.55812246304286e-07 | 1.32919279561061e-05 |
TAF1#6872 | 10 | 3.03913298704117 | 4.59104772732301e-05 | 0.00080707697962277 |
TAF7#6879 | 6 | 6.23621967541304 | 0.000140196002821237 | 0.00182886964010082 |
TBP#6908 | 10 | 3.36979153372399 | 1.6942293653553e-05 | 0.000390001368058942 |
THAP1#55145 | 3 | 8.55522125532309 | 0.004407746242643 | 0.0208828075592176 |
USF1#7391 | 9 | 5.20486304498833 | 2.37429471822852e-06 | 8.41143032825877e-05 |
USF2#7392 | 6 | 7.08665311912887 | 6.8302134157013e-05 | 0.00109040149636568 |
ZNF143#7702 | 6 | 7.3641144830334 | 5.49636173278436e-05 | 0.000930514707424649 |
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.