Coexpression cluster:C65
From FANTOM5_SSTAR
Full id: C65_CD14_Eosinophils_Monocytederived_Basophils_immature_Macrophage_Neutrophils
Phase1 CAGE Peaks
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:0044464 | cell part | 0.0110169370410131 |
| GO:0006357 | regulation of transcription from RNA polymerase II promoter | 0.0110169370410131 |
| GO:0006366 | transcription from RNA polymerase II promoter | 0.0110169370410131 |
| GO:0048523 | negative regulation of cellular process | 0.0110169370410131 |
| GO:0048519 | negative regulation of biological process | 0.0110169370410131 |
| GO:0016481 | negative regulation of transcription | 0.0110169370410131 |
| GO:0030228 | lipoprotein receptor activity | 0.0110169370410131 |
| GO:0005041 | low-density lipoprotein receptor activity | 0.0110169370410131 |
| GO:0045934 | negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0110169370410131 |
| GO:0045766 | positive regulation of angiogenesis | 0.0110169370410131 |
| GO:0009887 | organ morphogenesis | 0.0157805697684688 |
| GO:0005764 | lysosome | 0.0157805697684688 |
| GO:0000323 | lytic vacuole | 0.0157805697684688 |
| GO:0030169 | low-density lipoprotein binding | 0.0157805697684688 |
| GO:0031324 | negative regulation of cellular metabolic process | 0.0157805697684688 |
| GO:0016564 | transcription repressor activity | 0.0160788228917869 |
| GO:0030674 | protein binding, bridging | 0.0167097573713658 |
| GO:0005773 | vacuole | 0.0196882745563289 |
| GO:0009892 | negative regulation of metabolic process | 0.0227931743814195 |
| GO:0003714 | transcription corepressor activity | 0.0227931743814195 |
| GO:0016021 | integral to membrane | 0.0242153939333534 |
| GO:0031224 | intrinsic to membrane | 0.025159992169453 |
| GO:0044425 | membrane part | 0.0265856287196721 |
| GO:0008034 | lipoprotein binding | 0.0277528664170359 |
| GO:0044262 | cellular carbohydrate metabolic process | 0.0301222065828673 |
| GO:0001525 | angiogenesis | 0.0301222065828673 |
| GO:0003712 | transcription cofactor activity | 0.0308865182260587 |
| GO:0006167 | AMP biosynthetic process | 0.0308865182260587 |
| GO:0016656 | monodehydroascorbate reductase (NADH) activity | 0.0308865182260587 |
| GO:0030852 | regulation of granulocyte differentiation | 0.0308865182260587 |
| GO:0030854 | positive regulation of granulocyte differentiation | 0.0308865182260587 |
| GO:0005590 | collagen type VII | 0.0308865182260587 |
| GO:0008434 | vitamin D3 receptor activity | 0.0308865182260587 |
| GO:0005737 | cytoplasm | 0.0308865182260587 |
| GO:0005515 | protein binding | 0.0308865182260587 |
| GO:0048514 | blood vessel morphogenesis | 0.0308865182260587 |
| GO:0045765 | regulation of angiogenesis | 0.0308865182260587 |
| GO:0048646 | anatomical structure formation | 0.0335991407795975 |
| GO:0006898 | receptor-mediated endocytosis | 0.0340752893108384 |
| GO:0001568 | blood vessel development | 0.0378963848122442 |
| GO:0001944 | vasculature development | 0.0378963848122442 |
| GO:0003700 | transcription factor activity | 0.0378963848122442 |
| GO:0006916 | anti-apoptosis | 0.0378963848122442 |
| GO:0043565 | sequence-specific DNA binding | 0.0378963848122442 |
| GO:0016020 | membrane | 0.0378963848122442 |
| GO:0006670 | sphingosine metabolic process | 0.0378963848122442 |
| GO:0032422 | purine-rich negative regulatory element binding | 0.0378963848122442 |
| GO:0016889 | endodeoxyribonuclease activity, producing 3'-phosphomonoesters | 0.0378963848122442 |
| GO:0046033 | AMP metabolic process | 0.0378963848122442 |
| GO:0004531 | deoxyribonuclease II activity | 0.0378963848122442 |
| GO:0008481 | sphinganine kinase activity | 0.0378963848122442 |
| GO:0035238 | vitamin A biosynthetic process | 0.0378963848122442 |
| GO:0042362 | fat-soluble vitamin biosynthetic process | 0.0378963848122442 |
| GO:0019862 | IgA binding | 0.0378963848122442 |
| GO:0042905 | 9-cis-retinoic acid metabolic process | 0.0378963848122442 |
| GO:0042904 | 9-cis-retinoic acid biosynthetic process | 0.0378963848122442 |
| GO:0047035 | 3-alpha(17-beta)-hydroxysteroid dehydrogenase (NAD+) activity | 0.0378963848122442 |
| GO:0009605 | response to external stimulus | 0.0386290112645299 |
| GO:0006629 | lipid metabolic process | 0.0427264398054781 |
| GO:0010324 | membrane invagination | 0.0427264398054781 |
| GO:0006897 | endocytosis | 0.0427264398054781 |
| GO:0045892 | negative regulation of transcription, DNA-dependent | 0.045600196476447 |
| GO:0005624 | membrane fraction | 0.045600196476447 |
| GO:0005667 | transcription factor complex | 0.045600196476447 |
| GO:0009611 | response to wounding | 0.045600196476447 |
| GO:0015038 | glutathione disulfide oxidoreductase activity | 0.045600196476447 |
| GO:0017050 | D-erythro-sphingosine kinase activity | 0.045600196476447 |
| GO:0004566 | beta-glucuronidase activity | 0.045600196476447 |
| GO:0004019 | adenylosuccinate synthase activity | 0.045600196476447 |
| GO:0007207 | muscarinic acetylcholine receptor, phospholipase C activating pathway | 0.045600196476447 |
| GO:0015037 | peptide disulfide oxidoreductase activity | 0.045600196476447 |
| GO:0006355 | regulation of transcription, DNA-dependent | 0.0460205566465812 |
| GO:0008134 | transcription factor binding | 0.0460205566465812 |
| GO:0008202 | steroid metabolic process | 0.0484657614488581 |
| GO:0006066 | alcohol metabolic process | 0.0484657614488581 |
| GO:0044424 | intracellular part | 0.0484657614488581 |
| GO:0000287 | magnesium ion binding | 0.0484657614488581 |
| GO:0043066 | negative regulation of apoptosis | 0.0484657614488581 |
| GO:0044451 | nucleoplasm part | 0.0484657614488581 |
| GO:0043069 | negative regulation of programmed cell death | 0.0484657614488581 |
| GO:0009653 | anatomical structure morphogenesis | 0.0484657614488581 |
| GO:0048247 | lymphocyte chemotaxis | 0.0484657614488581 |
| GO:0001892 | embryonic placenta development | 0.0484657614488581 |
| GO:0031958 | corticosteroid receptor signaling pathway | 0.0484657614488581 |
| GO:0009249 | protein lipoylation | 0.0484657614488581 |
| GO:0042448 | progesterone metabolic process | 0.0484657614488581 |
| GO:0030851 | granulocyte differentiation | 0.0484657614488581 |
| GO:0045987 | positive regulation of smooth muscle contraction | 0.0484657614488581 |
| GO:0042921 | glucocorticoid receptor signaling pathway | 0.0484657614488581 |
| GO:0006351 | transcription, DNA-dependent | 0.0486981554268126 |
| GO:0032774 | RNA biosynthetic process | 0.0489477032778742 |
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 |
|---|---|---|
| bone marrow | 2.99e-87 | 76 |
| hematopoietic system | 4.74e-81 | 98 |
| blood island | 4.74e-81 | 98 |
| bone element | 4.00e-80 | 82 |
| immune system | 1.08e-75 | 93 |
| hemolymphoid system | 1.58e-72 | 108 |
| skeletal element | 4.40e-72 | 90 |
| skeletal system | 8.02e-64 | 100 |
| musculoskeletal system | 7.73e-34 | 167 |
| lateral plate mesoderm | 3.35e-33 | 203 |
| mesoderm | 3.72e-18 | 315 |
| mesoderm-derived structure | 3.72e-18 | 315 |
| presumptive mesoderm | 3.72e-18 | 315 |
| connective tissue | 1.44e-14 | 371 |
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 |
|---|---|---|---|---|
| EBF1#1879 | 48 | 1.53780722530688 | 0.00171907630759913 | 0.0106601716238776 |
| ESR1#2099 | 19 | 2.1028901533343 | 0.00209549742213237 | 0.012120716397324 |
| FOS#2353 | 57 | 1.84490450578051 | 3.92048656211706e-06 | 0.000127555045501852 |
| FOSL1#8061 | 22 | 3.14280127251873 | 2.94797947448122e-06 | 0.000101011820319995 |
| FOSL2#2355 | 27 | 1.64430005871642 | 0.00813652341302652 | 0.0321322834732314 |
| JUN#3725 | 40 | 1.800407078034 | 0.000226326205530778 | 0.00249733571890427 |
| JUND#3727 | 56 | 1.40899705303877 | 0.00474977054067265 | 0.0223259951166709 |
| MAFK#7975 | 22 | 2.14466233464841 | 0.000740759571979537 | 0.00583484342242785 |
| MAX#4149 | 65 | 1.50869103627864 | 0.000373222409626671 | 0.0037101632628022 |
| NFE2#4778 | 10 | 2.77713167811615 | 0.00373730794175249 | 0.0186248367671274 |
| SPI1#6688 | 69 | 2.03632489959737 | 5.5508121718546e-09 | 4.42535322455208e-07 |
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
