Coexpression cluster:C750
From FANTOM5_SSTAR
Full id: C750_Smooth_Mesenchymal_Fibroblast_Hepatic_Chondrocyte_Lens_tenocyte
Phase1 CAGE Peaks
| Hg19::chr12:6937564..6937585,+ | p1@LEPREL2 |
| Hg19::chr17:39968182..39968244,- | p1@LEPREL4 |
| Hg19::chr17:39968926..39968976,+ | p2@FKBP10 |
| Hg19::chr17:39969232..39969265,+ | p1@FKBP10 |
| Hg19::chr19:50031252..50031285,+ | p1@RCN3 |
| Hg19::chr19:50031567..50031632,+ | p2@RCN3 |
| Hg19::chr1:11994715..11994833,+ | p1@PLOD1 |
| Hg19::chr1:12014885..12014920,+ | p@chr1:12014885..12014920 + |
| Hg19::chr1:43232649..43232715,- | p1@LEPRE1 |
| Hg19::chr7:150929550..150929619,+ | p1@CHPF2 |
| Hg19::chrX:51636712..51636759,+ | p1@MAGED1 |
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:0031418 | L-ascorbic acid binding | 6.16739262198812e-07 |
| GO:0016706 | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors | 2.05166582405436e-06 |
| GO:0019797 | procollagen-proline 3-dioxygenase activity | 2.05166582405436e-06 |
| GO:0031544 | peptidyl-proline 3-dioxygenase activity | 2.05166582405436e-06 |
| GO:0005783 | endoplasmic reticulum | 2.05166582405436e-06 |
| GO:0051213 | dioxygenase activity | 4.09714468760063e-06 |
| GO:0016702 | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen | 4.09714468760063e-06 |
| GO:0016701 | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen | 4.09714468760063e-06 |
| GO:0019798 | procollagen-proline dioxygenase activity | 5.67381898068508e-06 |
| GO:0031543 | peptidyl-proline dioxygenase activity | 7.14845068613665e-06 |
| GO:0016705 | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | 3.27411397309372e-05 |
| GO:0019842 | vitamin binding | 7.96121713291799e-05 |
| GO:0005788 | endoplasmic reticulum lumen | 0.00052552777865081 |
| GO:0005506 | iron ion binding | 0.000584123997613624 |
| GO:0044432 | endoplasmic reticulum part | 0.000601781767003522 |
| GO:0005737 | cytoplasm | 0.000932935717654791 |
| GO:0046946 | hydroxylysine metabolic process | 0.00128537226735743 |
| GO:0046947 | hydroxylysine biosynthetic process | 0.00128537226735743 |
| GO:0044444 | cytoplasmic part | 0.00165350468860902 |
| GO:0008475 | procollagen-lysine 5-dioxygenase activity | 0.00346999433782819 |
| GO:0008285 | negative regulation of cell proliferation | 0.00401542118850137 |
| GO:0043169 | cation binding | 0.00767490924381294 |
| GO:0046872 | metal ion binding | 0.00938806226834687 |
| GO:0016491 | oxidoreductase activity | 0.00938806226834687 |
| GO:0043167 | ion binding | 0.00938806226834687 |
| GO:0030867 | rough endoplasmic reticulum membrane | 0.00978140308676731 |
| GO:0050680 | negative regulation of epithelial cell proliferation | 0.0102746571907546 |
| GO:0042127 | regulation of cell proliferation | 0.0128654976873371 |
| GO:0009067 | aspartate family amino acid biosynthetic process | 0.0130046817132735 |
| GO:0005791 | rough endoplasmic reticulum | 0.0130046817132735 |
| GO:0044424 | intracellular part | 0.0130046817132735 |
| GO:0009066 | aspartate family amino acid metabolic process | 0.0202044284172302 |
| GO:0050678 | regulation of epithelial cell proliferation | 0.0208221240785165 |
| GO:0043231 | intracellular membrane-bound organelle | 0.0208221240785165 |
| GO:0043227 | membrane-bound organelle | 0.0208221240785165 |
| GO:0050673 | epithelial cell proliferation | 0.0211587578541618 |
| GO:0008283 | cell proliferation | 0.0240554820540468 |
| GO:0005622 | intracellular | 0.0245856893432835 |
| GO:0001666 | response to hypoxia | 0.028377623610498 |
| GO:0019538 | protein metabolic process | 0.0322888692633528 |
| GO:0031974 | membrane-enclosed lumen | 0.0353706228375008 |
| GO:0043233 | organelle lumen | 0.0353706228375008 |
| GO:0043229 | intracellular organelle | 0.0420348181285098 |
| GO:0043226 | organelle | 0.0420348181285098 |
| GO:0008652 | amino acid biosynthetic process | 0.0429255537871426 |
| GO:0048523 | negative regulation of cellular process | 0.0433668328287759 |
| GO:0003755 | peptidyl-prolyl cis-trans isomerase activity | 0.0433668328287759 |
| GO:0016859 | cis-trans isomerase activity | 0.0433668328287759 |
| GO:0048519 | negative regulation of biological process | 0.0433668328287759 |
| GO:0043170 | macromolecule metabolic process | 0.0433668328287759 |
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 |
|---|---|---|
| non-terminally differentiated cell | 1.05e-51 | 180 |
| mesodermal cell | 8.64e-27 | 119 |
| contractile cell | 4.05e-24 | 59 |
| fibroblast | 1.07e-23 | 75 |
| muscle precursor cell | 2.85e-23 | 57 |
| myoblast | 2.85e-23 | 57 |
| multi-potent skeletal muscle stem cell | 2.85e-23 | 57 |
| muscle cell | 3.10e-22 | 54 |
| embryonic cell | 5.40e-22 | 248 |
| smooth muscle cell | 3.98e-20 | 42 |
| smooth muscle myoblast | 3.98e-20 | 42 |
| electrically responsive cell | 4.58e-20 | 60 |
| electrically active cell | 4.58e-20 | 60 |
| vascular associated smooth muscle cell | 6.13e-17 | 32 |
| somatic cell | 3.82e-12 | 591 |
| animal cell | 2.93e-10 | 679 |
| eukaryotic cell | 2.93e-10 | 679 |
| skin fibroblast | 5.17e-09 | 23 |
| cardiocyte | 1.28e-07 | 16 |
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) |
|---|---|
|
{{{tfbs_overrepresentation_jaspar}}} |
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 |
|---|---|---|---|---|
| FOSL1#8061 | 3 | 10.8309762862835 | 0.00226201738972272 | 0.0128441708348421 |
| HEY1#23462 | 8 | 2.93826257680415 | 0.00110599738805138 | 0.00768575828136922 |
| IRF1#3659 | 5 | 3.47143806980177 | 0.00894716207586585 | 0.0339337131873971 |
| POLR2A#5430 | 10 | 1.95223016050734 | 0.0030407318184143 | 0.0161350975705401 |
| TAF1#6872 | 8 | 2.43130638963294 | 0.00420424418913911 | 0.0200176457200592 |
| TBP#6908 | 7 | 2.35885407360679 | 0.011797348605664 | 0.0429798475957352 |
| ZNF143#7702 | 5 | 6.1367620691945 | 0.000703713135463718 | 0.00565782110505737 |
| ZNF263#10127 | 5 | 3.73720074409576 | 0.00651090818209497 | 0.027878838080842 |
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.
