Coexpression cluster:C821
From FANTOM5_SSTAR
Full id: C821_migratory_CD14_immature_CD14CD16_Dendritic_Macrophage_Monocytederived
Phase1 CAGE Peaks
| Hg19::chr12:69719024..69719043,- | p@chr12:69719024..69719043 - |
| Hg19::chr17:4643087..4643113,+ | p2@ZMYND15 |
| Hg19::chr17:4643118..4643145,+ | p1@ZMYND15 |
| Hg19::chr18:56203944..56203982,- | p17@ALPK2 |
| Hg19::chr3:121774202..121774222,+ | p1@CD86 |
| Hg19::chr3:121774295..121774306,+ | p3@CD86 |
| Hg19::chr3:121821281..121821283,+ | p@chr3:121821281..121821283 + |
| Hg19::chr7:6414211..6414222,+ | p2@RAC1 |
| Hg19::chr8:39771339..39771352,+ | p4@IDO1 |
| Hg19::chr8:623777..623823,- | p2@ERICH1 |
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 |
|---|---|---|---|---|
| 0.000187878492077518 | 0.0396423618283563 | 2 | 102 | Toll-like receptor signaling pathway (KEGG):04620 |
| 9.34899905302393e-05 | 0.0396423618283563 | 2 | 72 | Viral myocarditis (KEGG):05416 |
| 0.000187878492077518 | 0.0396423618283563 | 2 | 102 | Toll-like receptor signaling pathway (Wikipathways):WP75 |
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:0043016 | regulation of lymphotoxin A biosynthetic process | 0.00753461939402311 |
| GO:0043017 | positive regulation of lymphotoxin A biosynthetic process | 0.00753461939402311 |
| GO:0048261 | negative regulation of receptor-mediated endocytosis | 0.00753461939402311 |
| GO:0045630 | positive regulation of T-helper 2 cell differentiation | 0.00753461939402311 |
| GO:0035025 | positive regulation of Rho protein signal transduction | 0.00753461939402311 |
| GO:0045404 | positive regulation of interleukin-4 biosynthetic process | 0.00753461939402311 |
| GO:0045402 | regulation of interleukin-4 biosynthetic process | 0.00753461939402311 |
| GO:0032641 | lymphotoxin A production | 0.00753461939402311 |
| GO:0042109 | lymphotoxin A biosynthetic process | 0.00753461939402311 |
| GO:0042097 | interleukin-4 biosynthetic process | 0.00753461939402311 |
| GO:0045624 | positive regulation of T-helper cell differentiation | 0.00753461939402311 |
| GO:0045628 | regulation of T-helper 2 cell differentiation | 0.00753461939402311 |
| GO:0045806 | negative regulation of endocytosis | 0.00753461939402311 |
| GO:0032633 | interleukin-4 production | 0.00753461939402311 |
| GO:0045064 | T-helper 2 cell differentiation | 0.0082406260734007 |
| GO:0031529 | ruffle organization and biogenesis | 0.0082406260734007 |
| GO:0045622 | regulation of T-helper cell differentiation | 0.00852921161836958 |
| GO:0048259 | regulation of receptor-mediated endocytosis | 0.00852921161836958 |
| GO:0030032 | lamellipodium biogenesis | 0.00852921161836958 |
| GO:0051057 | positive regulation of small GTPase mediated signal transduction | 0.00852921161836958 |
| GO:0002294 | CD4-positive, alpha-beta T cell differentiation during immune response | 0.00852921161836958 |
| GO:0002292 | T cell differentiation during immune response | 0.00852921161836958 |
| GO:0042093 | T-helper cell differentiation | 0.00852921161836958 |
| GO:0002366 | leukocyte activation during immune response | 0.00852921161836958 |
| GO:0042092 | T-helper 2 type immune response | 0.00852921161836958 |
| GO:0002285 | lymphocyte activation during immune response | 0.00852921161836958 |
| GO:0002293 | alpha-beta T cell differentiation during immune response | 0.00852921161836958 |
| GO:0002286 | T cell activation during immune response | 0.00852921161836958 |
| GO:0002263 | cell activation during immune response | 0.00852921161836958 |
| GO:0030742 | GTP-dependent protein binding | 0.00852921161836958 |
| GO:0005041 | low-density lipoprotein receptor activity | 0.00852921161836958 |
| GO:0043367 | CD4-positive, alpha beta T cell differentiation | 0.00852921161836958 |
| GO:0045086 | positive regulation of interleukin-2 biosynthetic process | 0.00852921161836958 |
| GO:0030228 | lipoprotein receptor activity | 0.00852921161836958 |
| GO:0045076 | regulation of interleukin-2 biosynthetic process | 0.0110977673958521 |
| GO:0015026 | coreceptor activity | 0.0110977673958521 |
| GO:0042094 | interleukin-2 biosynthetic process | 0.0110977673958521 |
| GO:0046632 | alpha-beta T cell differentiation | 0.0110977673958521 |
| GO:0030169 | low-density lipoprotein binding | 0.0114885274969046 |
| GO:0046631 | alpha-beta T cell activation | 0.0125180103570752 |
| GO:0032623 | interleukin-2 production | 0.0134970475465134 |
| GO:0008034 | lipoprotein binding | 0.0181885724770088 |
| GO:0051051 | negative regulation of transport | 0.0185575468569413 |
| GO:0030041 | actin filament polymerization | 0.0185575468569413 |
| GO:0030100 | regulation of endocytosis | 0.0198985033483514 |
| GO:0042108 | positive regulation of cytokine biosynthetic process | 0.0224885972698191 |
| GO:0030217 | T cell differentiation | 0.0224885972698191 |
| GO:0006898 | receptor-mediated endocytosis | 0.0224885972698191 |
| GO:0030031 | cell projection biogenesis | 0.0268547456505492 |
| GO:0045727 | positive regulation of translation | 0.0278930136771611 |
| GO:0042035 | regulation of cytokine biosynthetic process | 0.0302754135134063 |
| GO:0031328 | positive regulation of cellular biosynthetic process | 0.0302754135134063 |
| GO:0008154 | actin polymerization and/or depolymerization | 0.0302754135134063 |
| GO:0030098 | lymphocyte differentiation | 0.0311720084080662 |
| GO:0042089 | cytokine biosynthetic process | 0.0319317503155234 |
| GO:0042107 | cytokine metabolic process | 0.0319317503155234 |
| GO:0009891 | positive regulation of biosynthetic process | 0.0322913838427321 |
| GO:0005044 | scavenger receptor activity | 0.0326458682279682 |
| GO:0002250 | adaptive immune response | 0.0326458682279682 |
| GO:0008009 | chemokine activity | 0.0326458682279682 |
| GO:0002460 | adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 0.0326458682279682 |
| GO:0042379 | chemokine receptor binding | 0.0326458682279682 |
| GO:0048770 | pigment granule | 0.0340809899234666 |
| GO:0042470 | melanosome | 0.0340809899234666 |
| GO:0051247 | positive regulation of protein metabolic process | 0.0343622254130415 |
| GO:0002521 | leukocyte differentiation | 0.0358243535923532 |
| GO:0051258 | protein polymerization | 0.0378480464406347 |
| GO:0042110 | T cell activation | 0.0378480464406347 |
| GO:0001664 | G-protein-coupled receptor binding | 0.0395726775772995 |
| GO:0051049 | regulation of transport | 0.0412468429366429 |
| GO:0001816 | cytokine production | 0.0417694350402286 |
| GO:0044267 | cellular protein metabolic process | 0.0484331498350187 |
| GO:0044260 | cellular macromolecule metabolic process | 0.0495517687458814 |
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>
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 | 0.312279 |
| MA0004.1 | 0.380329 |
| MA0006.1 | 0.236135 |
| MA0007.1 | 0.363007 |
| MA0009.1 | 0.828613 |
| MA0014.1 | 0.462516 |
| MA0017.1 | 0.270554 |
| MA0019.1 | 0.520264 |
| MA0024.1 | 0.725404 |
| MA0025.1 | 0.960689 |
| MA0027.1 | 2.43535 |
| MA0028.1 | 0.25013 |
| MA0029.1 | 0.744375 |
| MA0030.1 | 0.733118 |
| MA0031.1 | 0.669876 |
| MA0038.1 | 0.477043 |
| MA0040.1 | 0.750125 |
| MA0041.1 | 0.397617 |
| MA0042.1 | 0.367902 |
| MA0043.1 | 0.828925 |
| MA0046.1 | 0.817858 |
| MA0048.1 | 0.480635 |
| MA0050.1 | 4.58274 |
| MA0051.1 | 2.0713 |
| MA0052.1 | 0.753928 |
| MA0055.1 | 0.0662377 |
| MA0056.1 | 0 |
| MA0057.1 | 0.211138 |
| MA0058.1 | 0.293055 |
| MA0059.1 | 0.291897 |
| MA0060.1 | 0.138988 |
| MA0061.1 | 0.118318 |
| MA0063.1 | 0 |
| MA0066.1 | 0.477449 |
| MA0067.1 | 1.1435 |
| MA0068.1 | 0.631708 |
| MA0069.1 | 0.814052 |
| MA0070.1 | 0.803003 |
| MA0071.1 | 0.440254 |
| MA0072.1 | 0.798564 |
| MA0073.1 | 0.000749839 |
| MA0074.1 | 0.4723 |
| MA0076.1 | 0.307383 |
| MA0077.1 | 0.790956 |
| MA0078.1 | 0.568317 |
| MA0081.1 | 1.44489 |
| MA0083.1 | 0.836033 |
| MA0084.1 | 1.32998 |
| MA0087.1 | 0.79615 |
| MA0088.1 | 0.126492 |
| MA0089.1 | 0 |
| MA0090.1 | 0.320494 |
| MA0091.1 | 0.382762 |
| MA0092.1 | 0.918839 |
| MA0093.1 | 0.238771 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.49029 |
| MA0101.1 | 0.241637 |
| MA0103.1 | 0.646502 |
| MA0105.1 | 0.0508589 |
| MA0106.1 | 0.516528 |
| MA0107.1 | 0.529721 |
| MA0108.2 | 0.666881 |
| MA0109.1 | 0 |
| MA0111.1 | 0.885497 |
| MA0113.1 | 0.532314 |
| MA0114.1 | 0.174997 |
| MA0115.1 | 1.06753 |
| MA0116.1 | 0.182037 |
| MA0117.1 | 0.865782 |
| MA0119.1 | 0.277531 |
| MA0122.1 | 0.891407 |
| MA0124.1 | 1.0263 |
| MA0125.1 | 0.942948 |
| MA0130.1 | 0 |
| MA0131.1 | 0.585907 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.858623 |
| MA0136.1 | 1.21476 |
| MA0139.1 | 0.109245 |
| MA0140.1 | 0.437738 |
| MA0141.1 | 0.290336 |
| MA0142.1 | 0.638837 |
| MA0143.1 | 0.532484 |
| MA0144.1 | 0.163394 |
| MA0145.1 | 0.332712 |
| MA0146.1 | 0.0169564 |
| MA0147.1 | 0.184931 |
| MA0148.1 | 1.04145 |
| MA0149.1 | 0.428597 |
| MA0062.2 | 0.366815 |
| MA0035.2 | 1.11424 |
| MA0039.2 | 0.0317541 |
| MA0138.2 | 0.569505 |
| MA0002.2 | 0.407187 |
| MA0137.2 | 0.255808 |
| MA0104.2 | 0.138396 |
| MA0047.2 | 0.504873 |
| MA0112.2 | 0.0329985 |
| MA0065.2 | 0.0371828 |
| MA0150.1 | 0.315136 |
| MA0151.1 | 0 |
| MA0152.1 | 0.443956 |
| MA0153.1 | 0.926242 |
| MA0154.1 | 0.0494985 |
| MA0155.1 | 0.030416 |
| MA0156.1 | 0.715501 |
| MA0157.1 | 0.612166 |
| MA0158.1 | 0 |
| MA0159.1 | 0.185458 |
| MA0160.1 | 0.417847 |
| MA0161.1 | 0 |
| MA0162.1 | 1.23231 |
| MA0163.1 | 0.0235237 |
| MA0164.1 | 0.544294 |
| MA0080.2 | 1.24809 |
| MA0018.2 | 0.517858 |
| MA0099.2 | 0.444294 |
| MA0079.2 | 0.00464855 |
| MA0102.2 | 1.36707 |
| MA0258.1 | 0.155735 |
| MA0259.1 | 0.191914 |
| 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 |
|---|---|---|---|---|
| BATF#10538 | 3 | 7.30734053769109 | 0.00667851738648644 | 0.0284147829603315 |
| BDP1#55814 | 1 | 105.015340909091 | 0.0094819471733889 | 0.0357245700159294 |
| IRF4#3662 | 3 | 6.57435380602324 | 0.00894914180685731 | 0.033936292115986 |
| PAX5#5079 | 5 | 3.33478276558891 | 0.00985362449367583 | 0.0370314029685142 |
| SPI1#6688 | 6 | 4.92259410511364 | 0.000443419790230525 | 0.00412931961407809 |
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.
