Coexpression cluster:C187
From FANTOM5_SSTAR
Full id: C187_migratory_immature_Dendritic_CD19_CD14_Monocytederived_Macrophage
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
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 5.94382887969353e-18 | 2.35152730052875e-16 | 8 | 156 | Phagosome (KEGG):04145 |
| 1.93098502014593e-18 | 8.7308108410884e-17 | 8 | 136 | Cell adhesion molecules (CAMs) (KEGG):04514 |
| 5.26434142643762e-24 | 2.05539956434154e-21 | 9 | 78 | Antigen processing and presentation (KEGG):04612 |
| 2.34619914904252e-06 | 7.07211457782818e-05 | 3 | 88 | Hematopoietic cell lineage (KEGG):04640 |
| 3.71045711134679e-22 | 3.91453225247086e-20 | 8 | 49 | Intestinal immune network for IgA production (KEGG):04672 |
| 1.77370191667564e-22 | 2.24550662651136e-20 | 8 | 45 | Type I diabetes mellitus (KEGG):04940 |
| 1.10513356590572e-20 | 6.99549547218323e-19 | 8 | 73 | Leishmaniasis (KEGG):05140 |
| 1.60777920556184e-18 | 7.82864797785112e-17 | 8 | 133 | Toxoplasmosis (KEGG):05145 |
| 1.16846740185803e-21 | 9.24549831720164e-20 | 8 | 56 | Staphylococcus aureus infection (KEGG):05150 |
| 1.42563757096418e-20 | 8.20389620382114e-19 | 9 | 182 | Tuberculosis (KEGG):05152 |
| 1.59233395404391e-17 | 5.9291023112341e-16 | 8 | 176 | Influenza A (KEGG):05164 |
| 6.4941534418374e-24 | 2.05539956434154e-21 | 8 | 31 | Asthma (KEGG):05310 |
| 8.5591783060609e-22 | 7.73994266819507e-20 | 8 | 54 | Autoimmune thyroid disease (KEGG):05320 |
| 2.17679901415651e-18 | 9.18609183974046e-17 | 8 | 138 | Systemic lupus erythematosus (KEGG):05322 |
| 7.6480321605904e-20 | 4.03433696471143e-18 | 8 | 92 | Rheumatoid arthritis (KEGG):05323 |
| 5.06349289326769e-23 | 1.06839700047948e-20 | 8 | 39 | Allograft rejection (KEGG):05330 |
| 1.19329207042133e-22 | 1.88838470144176e-20 | 8 | 43 | Graft-versus-host disease (KEGG):05332 |
| 9.84053750225105e-21 | 6.9211780432499e-19 | 8 | 72 | Viral myocarditis (KEGG):05416 |
| 2.22785252343004e-05 | 0.000641013930605097 | 2 | 23 | Cytokines and Inflammatory Response (Wikipathways):WP530 |
| 1.97379666323609e-11 | 6.94118493238026e-10 | 7 | 511 | Signaling in Immune system (Reactome):REACT_6900 |
| 7.87387450514271e-09 | 2.49208128087767e-07 | 3 | 14 | {CD4,14} (Static Module):NA |
| 6.46443797065419e-10 | 2.15367854496006e-08 | 6 | 406 | {GRB2,414} (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:0002504 | antigen processing and presentation of peptide or polysaccharide antigen via MHC class II | 3.33465469112867e-15 |
| GO:0042613 | MHC class II protein complex | 7.24859124767789e-15 |
| GO:0019882 | antigen processing and presentation | 2.10238166781827e-14 |
| GO:0042611 | MHC protein complex | 4.28799775432895e-12 |
| GO:0006955 | immune response | 5.98637520332393e-11 |
| GO:0002376 | immune system process | 1.70644799795459e-10 |
| GO:0044459 | plasma membrane part | 9.03430251421799e-07 |
| GO:0043234 | protein complex | 3.96528655498425e-06 |
| GO:0005886 | plasma membrane | 2.44804717330264e-05 |
| GO:0032991 | macromolecular complex | 2.48418984192689e-05 |
| GO:0016021 | integral to membrane | 2.68591686971208e-05 |
| GO:0031224 | intrinsic to membrane | 2.68591686971208e-05 |
| GO:0044425 | membrane part | 7.19850934887258e-05 |
| GO:0032395 | MHC class II receptor activity | 7.19850934887258e-05 |
| GO:0016020 | membrane | 0.000415486121188224 |
| GO:0042289 | MHC class II protein binding | 0.00688692842383888 |
| GO:0043030 | regulation of macrophage activation | 0.00688692842383888 |
| GO:0005764 | lysosome | 0.00688692842383888 |
| GO:0000323 | lytic vacuole | 0.00688692842383888 |
| GO:0005773 | vacuole | 0.00867876218897856 |
| GO:0045058 | T cell selection | 0.0130909043296571 |
| GO:0042116 | macrophage activation | 0.0130909043296571 |
| GO:0046457 | prostanoid biosynthetic process | 0.0133319549255772 |
| GO:0001516 | prostaglandin biosynthetic process | 0.0133319549255772 |
| GO:0006693 | prostaglandin metabolic process | 0.0209058329785795 |
| GO:0006692 | prostanoid metabolic process | 0.0209058329785795 |
| GO:0019883 | antigen processing and presentation of endogenous antigen | 0.0213135556485108 |
| GO:0042287 | MHC protein binding | 0.0262478235200968 |
| GO:0002274 | myeloid leukocyte activation | 0.0297379024138541 |
| GO:0031902 | late endosome membrane | 0.0308696602270396 |
| GO:0046456 | icosanoid biosynthetic process | 0.033980396421052 |
| GO:0030217 | T cell differentiation | 0.0408650733729104 |
| GO:0006690 | icosanoid metabolic process | 0.0447742305917279 |
| GO:0005765 | lysosomal membrane | 0.0447742305917279 |
| GO:0016064 | immunoglobulin mediated immune response | 0.0447742305917279 |
| GO:0005770 | late endosome | 0.0447742305917279 |
| GO:0019724 | B cell mediated immunity | 0.0447742305917279 |
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 |
|---|---|---|
| hematopoietic system | 4.94e-51 | 98 |
| blood island | 4.94e-51 | 98 |
| hemolymphoid system | 3.00e-46 | 108 |
| bone marrow | 4.30e-38 | 76 |
| immune system | 2.80e-36 | 93 |
| bone element | 1.89e-33 | 82 |
| skeletal element | 2.81e-28 | 90 |
| adult organism | 1.16e-27 | 114 |
| skeletal system | 7.94e-24 | 100 |
| lateral plate mesoderm | 4.90e-16 | 203 |
| blood | 1.17e-10 | 15 |
| haemolymphatic fluid | 1.17e-10 | 15 |
| organism substance | 1.17e-10 | 15 |
| musculoskeletal system | 4.51e-08 | 167 |
| connective tissue | 5.64e-07 | 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) |
|---|---|
| MA0003.1 | 4.0701e-06 |
| MA0004.1 | 1.20795 |
| MA0006.1 | 0.00647075 |
| MA0007.1 | 0.0510684 |
| MA0009.1 | 0.367285 |
| MA0014.1 | 4.62099e-06 |
| MA0017.1 | 1.89508 |
| MA0019.1 | 0.0769485 |
| MA0024.1 | 0.0705712 |
| MA0025.1 | 0.185862 |
| MA0027.1 | 1.48276 |
| MA0028.1 | 0.00023646 |
| MA0029.1 | 3.23897 |
| MA0030.1 | 0.0734746 |
| MA0031.1 | 0.0515676 |
| MA0038.1 | 0.297678 |
| MA0040.1 | 0.577793 |
| MA0041.1 | 0.00415987 |
| MA0042.1 | 0.00267279 |
| MA0043.1 | 0.367676 |
| MA0046.1 | 2.34902 |
| MA0048.1 | 0.0106866 |
| MA0050.1 | 0.0167305 |
| MA0051.1 | 0.142598 |
| MA0052.1 | 0.0816217 |
| MA0055.1 | 0.644432 |
| MA0056.1 | 0 |
| MA0057.1 | 0.0725836 |
| MA0058.1 | 3.38263 |
| MA0059.1 | 0.484527 |
| MA0060.1 | 0.289338 |
| MA0061.1 | 0.123709 |
| MA0063.1 | 0 |
| MA0066.1 | 0.147373 |
| MA0067.1 | 0.307426 |
| MA0068.1 | 0.0835745 |
| MA0069.1 | 0.107693 |
| MA0070.1 | 0.102625 |
| MA0071.1 | 0.407721 |
| MA0072.1 | 0.100624 |
| MA0073.1 | 0.0110214 |
| MA0074.1 | 4.42185 |
| MA0076.1 | 0.00652466 |
| MA0077.1 | 0.321359 |
| MA0078.1 | 0.0254452 |
| MA0081.1 | 0.485145 |
| MA0083.1 | 0.118136 |
| MA0084.1 | 0.451809 |
| MA0087.1 | 1.11445 |
| MA0088.1 | 0.490568 |
| MA0089.1 | 0 |
| MA0090.1 | 0.840609 |
| MA0091.1 | 0.270958 |
| MA0092.1 | 1.30225 |
| MA0093.1 | 2.89695 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.0605826 |
| MA0101.1 | 0.183686 |
| MA0103.1 | 0.0170189 |
| MA0105.1 | 0.000882638 |
| MA0106.1 | 0.0747848 |
| MA0107.1 | 0.0647912 |
| MA0108.2 | 0.0506377 |
| MA0109.1 | 0 |
| MA0111.1 | 2.23563 |
| MA0113.1 | 0.0841685 |
| MA0114.1 | 2.12495 |
| MA0115.1 | 2.01591 |
| MA0116.1 | 0.0687893 |
| MA0117.1 | 0.133014 |
| MA0119.1 | 0.0911122 |
| MA0122.1 | 0.146496 |
| MA0124.1 | 0.226763 |
| MA0125.1 | 0.175391 |
| MA0130.1 | 0 |
| MA0131.1 | 1.22571 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.129356 |
| MA0136.1 | 3.40951 |
| MA0139.1 | 0.0166697 |
| MA0140.1 | 1.22622 |
| MA0141.1 | 0.671851 |
| MA0142.1 | 0.0424045 |
| MA0143.1 | 0.995709 |
| MA0144.1 | 0.937338 |
| MA0145.1 | 0.00742747 |
| MA0146.1 | 0.008046 |
| MA0147.1 | 0.204141 |
| MA0148.1 | 0.00451826 |
| MA0149.1 | 3.85392 |
| MA0062.2 | 0.57715 |
| MA0035.2 | 1.58773 |
| MA0039.2 | 2.59892e-06 |
| MA0138.2 | 0.493766 |
| MA0002.2 | 0.0634921 |
| MA0137.2 | 0.219533 |
| MA0104.2 | 0.198297 |
| MA0047.2 | 0.178725 |
| MA0112.2 | 0.22742 |
| MA0065.2 | 2.43295 |
| MA0150.1 | 1.06853 |
| MA0151.1 | 0 |
| MA0152.1 | 2.04913 |
| MA0153.1 | 0.165772 |
| MA0154.1 | 1.79724 |
| MA0155.1 | 0.00178624 |
| MA0156.1 | 2.43796 |
| MA0157.1 | 0.141167 |
| MA0158.1 | 0 |
| MA0159.1 | 3.37337 |
| MA0160.1 | 0.55778 |
| MA0161.1 | 0 |
| MA0162.1 | 2.08907e-12 |
| MA0163.1 | 0.00506747 |
| MA0164.1 | 1.43623 |
| MA0080.2 | 2.52158 |
| MA0018.2 | 0.075551 |
| MA0099.2 | 0.00760093 |
| MA0079.2 | 2.14563e-14 |
| MA0102.2 | 0.48239 |
| MA0258.1 | 0.11894 |
| MA0259.1 | 0.00201626 |
| 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 |
|---|---|---|---|---|
| BCL3#602 | 27 | 10.2502392934169 | 4.40179319354071e-20 | 1.12400703995159e-17 |
| BCLAF1#9774 | 26 | 6.1864707457491 | 3.91017816704815e-14 | 6.42099210044563e-12 |
| IRF4#3662 | 16 | 3.85310113173523 | 3.46807194950918e-06 | 0.000115534917491161 |
| POLR2A#5430 | 83 | 1.9586660841134 | 1.7046165343123e-19 | 4.13059039969936e-17 |
| POU2F2#5452 | 48 | 4.80323027221584 | 1.16950827676636e-22 | 3.35555700321983e-20 |
| ZBTB33#10009 | 16 | 5.56742418109559 | 2.6407718518275e-08 | 1.82286564066763e-06 |
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
