Coexpression cluster:C646
From FANTOM5_SSTAR
Full id: C646_CD14_Mast_vagina_thymus_MCF7_immature_Eosinophils
Phase1 CAGE Peaks
| Hg19::chr10:126847417..126847439,+ | p@chr10:126847417..126847439 + |
| Hg19::chr11:63953135..63953159,- | p@chr11:63953135..63953159 - |
| Hg19::chr12:1704640..1704649,+ | p@chr12:1704640..1704649 + |
| Hg19::chr12:1704650..1704671,+ | p@chr12:1704650..1704671 + |
| Hg19::chr13:31191642..31191749,- | p2@HMGB1 |
| Hg19::chr6:31782588..31782612,+ | p@chr6:31782588..31782612 + |
| Hg19::chr6:31782632..31782654,+ | p@chr6:31782632..31782654 + |
| Hg19::chr6:31790025..31790063,+ | p@chr6:31790025..31790063 + |
| Hg19::chr6:44215668..44215690,+ | p13@HSP90AB1 |
| Hg19::chr7:157129414..157129491,- | p@chr7:157129414..157129491 - |
| Hg19::chr7:641637..641649,+ | p@chr7:641637..641649 + |
| Hg19::chr9:33025026..33025046,- | p5@APTX |
| Hg19::chrX:118740549..118740569,+ | p@chrX:118740549..118740569 + |
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
No results for this coexpression
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:0006950 | response to stress | 0.00546884366603595 |
| GO:0033699 | DNA 5'-adenosine monophosphate hydrolase activity | 0.00546884366603595 |
| GO:0017055 | negative regulation of transcriptional preinitiation complex assembly | 0.00546884366603595 |
| GO:0035312 | 5'-3' exodeoxyribonuclease activity | 0.00546884366603595 |
| GO:0030911 | TPR domain binding | 0.00546884366603595 |
| GO:0006288 | base-excision repair, DNA ligation | 0.00546884366603595 |
| GO:0000785 | chromatin | 0.00546884366603595 |
| GO:0008409 | 5'-3' exonuclease activity | 0.00546884366603595 |
| GO:0030235 | nitric-oxide synthase regulator activity | 0.00546884366603595 |
| GO:0008967 | phosphoglycolate phosphatase activity | 0.00546884366603595 |
| GO:0006281 | DNA repair | 0.00546884366603595 |
| GO:0000012 | single strand break repair | 0.00546884366603595 |
| GO:0051103 | DNA ligation during DNA repair | 0.00546884366603595 |
| GO:0006974 | response to DNA damage stimulus | 0.00546884366603595 |
| GO:0051123 | transcriptional preinitiation complex assembly | 0.00546884366603595 |
| GO:0045898 | regulation of transcriptional preinitiation complex assembly | 0.00546884366603595 |
| GO:0044427 | chromosomal part | 0.00546884366603595 |
| GO:0016895 | exodeoxyribonuclease activity, producing 5'-phosphomonoesters | 0.00561185847523729 |
| GO:0004529 | exodeoxyribonuclease activity | 0.00561185847523729 |
| GO:0045429 | positive regulation of nitric oxide biosynthetic process | 0.00561185847523729 |
| GO:0009719 | response to endogenous stimulus | 0.00561185847523729 |
| GO:0005694 | chromosome | 0.00561185847523729 |
| GO:0006266 | DNA ligation | 0.00580392531463132 |
| GO:0045428 | regulation of nitric oxide biosynthetic process | 0.00598028115587165 |
| GO:0042221 | response to chemical stimulus | 0.00598028115587165 |
| GO:0008301 | DNA bending activity | 0.00627481473872941 |
| GO:0006268 | DNA unwinding during replication | 0.00878767242417505 |
| GO:0032392 | DNA geometric change | 0.00920378733858085 |
| GO:0032508 | DNA duplex unwinding | 0.00920378733858085 |
| GO:0042542 | response to hydrogen peroxide | 0.00959366799323775 |
| GO:0031647 | regulation of protein stability | 0.00959366799323775 |
| GO:0046209 | nitric oxide metabolic process | 0.00959366799323775 |
| GO:0016796 | exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters | 0.00959366799323775 |
| GO:0006809 | nitric oxide biosynthetic process | 0.00959366799323775 |
| GO:0008219 | cell death | 0.00981296665538481 |
| GO:0016265 | death | 0.00981296665538481 |
| GO:0000302 | response to reactive oxygen species | 0.0108178019051623 |
| GO:0006284 | base-excision repair | 0.0136508321545364 |
| GO:0047485 | protein N-terminus binding | 0.0148191578271127 |
| GO:0048468 | cell development | 0.0161969686070464 |
| GO:0006259 | DNA metabolic process | 0.0161969686070464 |
| GO:0003684 | damaged DNA binding | 0.0172259976547266 |
| GO:0004536 | deoxyribonuclease activity | 0.0172259976547266 |
| GO:0000793 | condensed chromosome | 0.0174464800683915 |
| GO:0003725 | double-stranded RNA binding | 0.0174464800683915 |
| GO:0051789 | response to protein stimulus | 0.0185918184031567 |
| GO:0006986 | response to unfolded protein | 0.0185918184031567 |
| GO:0009891 | positive regulation of biosynthetic process | 0.0215915490740713 |
| GO:0004527 | exonuclease activity | 0.0217539351273584 |
| GO:0048770 | pigment granule | 0.0240862170172025 |
| GO:0042470 | melanosome | 0.0240862170172025 |
| GO:0065007 | biological regulation | 0.0251203755349182 |
| GO:0048869 | cellular developmental process | 0.0255408107288152 |
| GO:0030154 | cell differentiation | 0.0255408107288152 |
| GO:0003690 | double-stranded DNA binding | 0.0290403494790685 |
| GO:0003682 | chromatin binding | 0.0311238690921357 |
| GO:0006979 | response to oxidative stress | 0.0311238690921357 |
| GO:0019904 | protein domain specific binding | 0.0318162727159351 |
| GO:0000122 | negative regulation of transcription from RNA polymerase II promoter | 0.0318162727159351 |
| GO:0044271 | nitrogen compound biosynthetic process | 0.0361915885977443 |
| GO:0043566 | structure-specific DNA binding | 0.0384906468708542 |
| GO:0006261 | DNA-dependent DNA replication | 0.0386682473302357 |
| GO:0005730 | nucleolus | 0.0386682473302357 |
| GO:0006916 | anti-apoptosis | 0.0392117309418119 |
| GO:0006310 | DNA recombination | 0.0433794383969251 |
| GO:0043231 | intracellular membrane-bound organelle | 0.0433794383969251 |
| GO:0043227 | membrane-bound organelle | 0.0433794383969251 |
| GO:0051082 | unfolded protein binding | 0.0433794383969251 |
| GO:0045892 | negative regulation of transcription, DNA-dependent | 0.0433881727652442 |
| GO:0005515 | protein binding | 0.0446881835055404 |
| GO:0009889 | regulation of biosynthetic process | 0.0450553585491057 |
| GO:0043066 | negative regulation of apoptosis | 0.0464283747168019 |
| GO:0043069 | negative regulation of programmed cell death | 0.0464283747168019 |
| GO:0043232 | intracellular non-membrane-bound organelle | 0.0467892241541275 |
| GO:0043228 | non-membrane-bound organelle | 0.0467892241541275 |
| GO:0004518 | nuclease activity | 0.0476754711706606 |
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 |
|---|---|---|
| classical monocyte | 4.76e-27 | 42 |
| CD14-positive, CD16-negative classical monocyte | 4.76e-27 | 42 |
| granulocyte monocyte progenitor cell | 1.61e-25 | 67 |
| defensive cell | 1.82e-23 | 48 |
| phagocyte | 1.82e-23 | 48 |
| myeloid lineage restricted progenitor cell | 2.94e-23 | 66 |
| macrophage dendritic cell progenitor | 3.50e-23 | 61 |
| myeloid leukocyte | 2.03e-22 | 72 |
| monopoietic cell | 1.55e-21 | 59 |
| monocyte | 1.55e-21 | 59 |
| monoblast | 1.55e-21 | 59 |
| promonocyte | 1.55e-21 | 59 |
| hematopoietic lineage restricted progenitor cell | 7.41e-16 | 120 |
| myeloid cell | 8.11e-16 | 108 |
| common myeloid progenitor | 8.11e-16 | 108 |
| leukocyte | 1.44e-14 | 136 |
| nongranular leukocyte | 4.53e-12 | 115 |
| hematopoietic oligopotent progenitor cell | 9.53e-12 | 161 |
| hematopoietic multipotent progenitor cell | 9.53e-12 | 161 |
| stuff accumulating cell | 3.06e-11 | 87 |
| hematopoietic stem cell | 4.20e-11 | 168 |
| angioblastic mesenchymal cell | 4.20e-11 | 168 |
| hematopoietic cell | 1.04e-10 | 177 |
| Ontology term | p-value | n |
|---|---|---|
| bone marrow | 5.28e-23 | 76 |
| bone element | 3.47e-21 | 82 |
| immune system | 8.22e-20 | 93 |
| hematopoietic system | 5.05e-18 | 98 |
| blood island | 5.05e-18 | 98 |
| skeletal element | 7.75e-18 | 90 |
| adult organism | 8.55e-18 | 114 |
| hemolymphoid system | 1.25e-15 | 108 |
| skeletal system | 1.79e-14 | 100 |
| neural tube | 4.76e-14 | 56 |
| neural rod | 4.76e-14 | 56 |
| future spinal cord | 4.76e-14 | 56 |
| neural keel | 4.76e-14 | 56 |
| regional part of nervous system | 4.08e-13 | 53 |
| regional part of brain | 4.08e-13 | 53 |
| regional part of forebrain | 5.32e-10 | 41 |
| forebrain | 5.32e-10 | 41 |
| anterior neural tube | 5.32e-10 | 41 |
| future forebrain | 5.32e-10 | 41 |
| brain | 3.30e-09 | 68 |
| future brain | 3.30e-09 | 68 |
| central nervous system | 9.78e-09 | 81 |
| neurectoderm | 4.52e-08 | 86 |
| neural plate | 1.10e-07 | 82 |
| presumptive neural plate | 1.10e-07 | 82 |
| brain grey matter | 1.44e-07 | 34 |
| gray matter | 1.44e-07 | 34 |
| telencephalon | 1.55e-07 | 34 |
| nervous system | 2.32e-07 | 89 |
| organ | 4.51e-07 | 503 |
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 | 0.0652591 |
| MA0004.1 | 0.297884 |
| MA0006.1 | 0.506155 |
| MA0007.1 | 0.771118 |
| MA0009.1 | 0.724811 |
| MA0014.1 | 0.369455 |
| MA0017.1 | 0.199401 |
| MA0019.1 | 0.428118 |
| MA0024.1 | 0.6245 |
| MA0025.1 | 0.854131 |
| MA0027.1 | 2.32165 |
| MA0028.1 | 1.02527 |
| MA0029.1 | 0.642879 |
| MA0030.1 | 0.63197 |
| MA0031.1 | 1.39986 |
| MA0038.1 | 0.387473 |
| MA0040.1 | 0.648455 |
| MA0041.1 | 0.313738 |
| MA0042.1 | 0.781261 |
| MA0043.1 | 0.725115 |
| MA0046.1 | 0.714324 |
| MA0048.1 | 0.565955 |
| MA0050.1 | 0.287284 |
| MA0051.1 | 0.383704 |
| MA0052.1 | 0.652145 |
| MA0055.1 | 0.083823 |
| MA0056.1 | 0 |
| MA0057.1 | 2.17648 |
| MA0058.1 | 0.625569 |
| MA0059.1 | 0.218203 |
| MA0060.1 | 0.622587 |
| MA0061.1 | 1.91627 |
| MA0063.1 | 0 |
| MA0066.1 | 0.387854 |
| MA0067.1 | 1.03434 |
| MA0068.1 | 0.760324 |
| MA0069.1 | 0.710614 |
| MA0070.1 | 2.80746 |
| MA0071.1 | 0.35315 |
| MA0072.1 | 0.695528 |
| MA0073.1 | 0.983715 |
| MA0074.1 | 0.383033 |
| MA0076.1 | 1.22198 |
| MA0077.1 | 0.688123 |
| MA0078.1 | 0.473657 |
| MA0081.1 | 0.218332 |
| MA0083.1 | 0.732051 |
| MA0084.1 | 1.21913 |
| MA0087.1 | 0.693179 |
| MA0088.1 | 0.854057 |
| MA0089.1 | 0 |
| MA0090.1 | 0.243681 |
| MA0091.1 | 0.30011 |
| MA0092.1 | 0.268302 |
| MA0093.1 | 0.511707 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.399896 |
| MA0101.1 | 0.17426 |
| MA0103.1 | 0.162663 |
| MA0105.1 | 1.15008 |
| MA0106.1 | 0.424592 |
| MA0107.1 | 0.77236 |
| MA0108.2 | 0.568002 |
| MA0109.1 | 0 |
| MA0111.1 | 1.30787 |
| MA0113.1 | 0.439505 |
| MA0114.1 | 0.118142 |
| MA0115.1 | 0.959312 |
| MA0116.1 | 0.123927 |
| MA0117.1 | 0.76111 |
| MA0119.1 | 0.593096 |
| MA0122.1 | 0.786181 |
| MA0124.1 | 0.918678 |
| MA0125.1 | 0.83671 |
| MA0130.1 | 0 |
| MA0131.1 | 1.22896 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.754112 |
| MA0136.1 | 1.02008 |
| MA0139.1 | 0.235473 |
| MA0140.1 | 0.350813 |
| MA0141.1 | 0.216821 |
| MA0142.1 | 0.541045 |
| MA0143.1 | 0.439666 |
| MA0144.1 | 0.35188 |
| MA0145.1 | 0.0753792 |
| MA0146.1 | 0.886077 |
| MA0147.1 | 0.397782 |
| MA0148.1 | 0.319209 |
| MA0149.1 | 0.342334 |
| MA0062.2 | 1.35421 |
| MA0035.2 | 0.350194 |
| MA0039.2 | 1.01865 |
| MA0138.2 | 0.474787 |
| MA0002.2 | 0.280231 |
| MA0137.2 | 0.186529 |
| MA0104.2 | 0.298328 |
| MA0047.2 | 0.413608 |
| MA0112.2 | 0.0147485 |
| MA0065.2 | 0.953721 |
| MA0150.1 | 0.238884 |
| MA0151.1 | 0 |
| MA0152.1 | 0.356591 |
| MA0153.1 | 0.820317 |
| MA0154.1 | 0.105196 |
| MA0155.1 | 1.18433 |
| MA0156.1 | 1.05198 |
| MA0157.1 | 0.515488 |
| MA0158.1 | 0 |
| MA0159.1 | 0.126752 |
| MA0160.1 | 0.332385 |
| MA0161.1 | 0 |
| MA0162.1 | 1.33143 |
| MA0163.1 | 1.65684 |
| MA0164.1 | 0.450848 |
| MA0080.2 | 0.511865 |
| MA0018.2 | 0.425847 |
| MA0099.2 | 0.356906 |
| MA0079.2 | 7.59016 |
| MA0102.2 | 1.25596 |
| MA0258.1 | 0.102521 |
| MA0259.1 | 0.132107 |
| 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 |
|---|---|---|---|---|
| CCNT2#905 | 10 | 4.87400121304818 | 1.72226346360207e-06 | 6.49824688855263e-05 |
| CHD2#1106 | 5 | 3.97847032081418 | 0.00558368656684048 | 0.0252524419241438 |
| E2F6#1876 | 8 | 3.08748045027531 | 0.00121584853405667 | 0.00818288471764043 |
| EGR1#1958 | 8 | 3.06964867372932 | 0.00126568416933679 | 0.00849202036241582 |
| ELF1#1997 | 8 | 2.62036797465079 | 0.00372565735117579 | 0.0185765266924209 |
| ELK4#2005 | 4 | 4.9955943564517 | 0.006554850858591 | 0.0280176012450022 |
| EP300#2033 | 6 | 3.12643464287225 | 0.00695371655281501 | 0.029409540903031 |
| ETS1#2113 | 6 | 4.49019734870877 | 0.00106508682285967 | 0.00752412085312775 |
| GTF2B#2959 | 4 | 9.82887074902284 | 0.000546622148132622 | 0.00472041264501595 |
| GTF2F1#2962 | 7 | 6.8598173951772 | 2.05623134739606e-05 | 0.000455269759785239 |
| HEY1#23462 | 9 | 2.79699995291934 | 0.000914123114219825 | 0.00665296891470413 |
| HSF1#3297 | 7 | 88.4642051282051 | 5.05042282057528e-13 | 7.35650082228817e-11 |
| IRF1#3659 | 7 | 4.11231894422672 | 0.000547579966104684 | 0.00472751129040317 |
| JUNB#3726 | 3 | 7.06399215226642 | 0.007792750127433 | 0.0320167989991729 |
| NFKB1#4790 | 7 | 2.95511107456591 | 0.0040713240829685 | 0.0194726605560152 |
| PBX3#5090 | 4 | 6.74292698053666 | 0.00222199559447697 | 0.0127752820199054 |
| POLR2A#5430 | 13 | 2.14745317655807 | 4.83928878402115e-05 | 0.000840529654605662 |
| PPARGC1A#10891 | 4 | 107.708041958042 | 4.61292015241441e-08 | 3.01482332789743e-06 |
| SIN3A#25942 | 8 | 3.32854444727085 | 0.000719146205919868 | 0.00574519319208025 |
| SRF#6722 | 5 | 5.3066070239107 | 0.00156826497609789 | 0.00994704395959477 |
| STAT2#6773 | 3 | 15.060870273794 | 0.00091606785034798 | 0.00666572913136576 |
| TAF1#6872 | 9 | 2.31441665936213 | 0.00394222869196859 | 0.0189515499360418 |
| TAF7#6879 | 6 | 5.27680126381104 | 0.000446292320197271 | 0.00415347742194642 |
| TBP#6908 | 8 | 2.28108965359778 | 0.00928530908545583 | 0.0350760804273853 |
| THAP1#55145 | 3 | 7.23903336988877 | 0.00728433784323498 | 0.0301378188016329 |
| WRNIP1#56897 | 3 | 25.3430686960099 | 0.000201329398099232 | 0.00239319838471269 |
| YY1#7528 | 7 | 2.64447655761361 | 0.00776069714688224 | 0.0319177541672534 |
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.
