Coexpression cluster:C67
From FANTOM5_SSTAR
Full id: C67_CD14_Monocytederived_Macrophage_dura_Dendritic_spleen_lung
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 |
|---|---|---|---|---|
| 1.37622863172383e-05 | 0.00435576361940593 | 4 | 69 | Complement and coagulation cascades (KEGG):04610 |
| 5.50736472127791e-05 | 0.0116205395618964 | 3 | 35 | Prion diseases (KEGG):05020 |
| 0.000226047348904476 | 0.0238479953094222 | 3 | 56 | Staphylococcus aureus infection (KEGG):05150 |
| 9.81038945513756e-06 | 0.00435576361940593 | 3 | 20 | Complement Activation, Classical Pathway (Wikipathways):WP545 |
| 0.000181297842375134 | 0.0229523068446919 | 3 | 52 | Complement and Coagulation Cascades (Wikipathways):WP558 |
| 0.000142738451715954 | 0.0225883599840498 | 3 | 48 | {FCGR2B,50} (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:0006954 | inflammatory response | 9.56206002322801e-06 |
| GO:0009611 | response to wounding | 9.56206002322801e-06 |
| GO:0006952 | defense response | 9.56206002322801e-06 |
| GO:0009605 | response to external stimulus | 1.51938267980098e-05 |
| GO:0005615 | extracellular space | 3.07428498430535e-05 |
| GO:0016021 | integral to membrane | 0.000151314087487177 |
| GO:0031224 | intrinsic to membrane | 0.000151314087487177 |
| GO:0044421 | extracellular region part | 0.000207241943640159 |
| GO:0044425 | membrane part | 0.000209503328142941 |
| GO:0005602 | complement component C1 complex | 0.000209503328142941 |
| GO:0006950 | response to stress | 0.000299723137100732 |
| GO:0051239 | regulation of multicellular organismal process | 0.000393696681900918 |
| GO:0006959 | humoral immune response | 0.000393696681900918 |
| GO:0002460 | adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 0.000393696681900918 |
| GO:0002250 | adaptive immune response | 0.000393696681900918 |
| GO:0004871 | signal transducer activity | 0.000393696681900918 |
| GO:0060089 | molecular transducer activity | 0.000393696681900918 |
| GO:0002526 | acute inflammatory response | 0.000395684962589794 |
| GO:0004872 | receptor activity | 0.000495322293292815 |
| GO:0006958 | complement activation, classical pathway | 0.000514381499063508 |
| GO:0002376 | immune system process | 0.000514381499063508 |
| GO:0032501 | multicellular organismal process | 0.000564258340408766 |
| GO:0002455 | humoral immune response mediated by circulating immunoglobulin | 0.000569596827366125 |
| GO:0006956 | complement activation | 0.0011672377328113 |
| GO:0002541 | activation of plasma proteins during acute inflammatory response | 0.0011672377328113 |
| GO:0016020 | membrane | 0.00215367171501412 |
| GO:0016064 | immunoglobulin mediated immune response | 0.00242847613547409 |
| GO:0019724 | B cell mediated immunity | 0.00248221664204666 |
| GO:0004888 | transmembrane receptor activity | 0.00250507284701867 |
| GO:0007610 | behavior | 0.00326835384677842 |
| GO:0007154 | cell communication | 0.0047357985380475 |
| GO:0002253 | activation of immune response | 0.00538923454415271 |
| GO:0007626 | locomotory behavior | 0.00538923454415271 |
| GO:0002449 | lymphocyte mediated immunity | 0.00538923454415271 |
| GO:0002443 | leukocyte mediated immunity | 0.00663145928499155 |
| GO:0051180 | vitamin transport | 0.00688061779508333 |
| GO:0005764 | lysosome | 0.00722821917545694 |
| GO:0000323 | lytic vacuole | 0.00722821917545694 |
| GO:0050778 | positive regulation of immune response | 0.00766383022390036 |
| GO:0002684 | positive regulation of immune system process | 0.00773329668652567 |
| GO:0042110 | T cell activation | 0.0107938376803848 |
| GO:0050776 | regulation of immune response | 0.0107938376803848 |
| GO:0005773 | vacuole | 0.0109283136920231 |
| GO:0002682 | regulation of immune system process | 0.0109283136920231 |
| GO:0004522 | pancreatic ribonuclease activity | 0.0115196513735499 |
| GO:0051240 | positive regulation of multicellular organismal process | 0.0120480891577337 |
| GO:0004714 | transmembrane receptor protein tyrosine kinase activity | 0.0131440773602587 |
| GO:0002252 | immune effector process | 0.0132156995203932 |
| GO:0045087 | innate immune response | 0.0143572766851503 |
| GO:0016892 | endoribonuclease activity, producing 3'-phosphomonoesters | 0.0154083646696484 |
| GO:0016894 | endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters | 0.017347446752541 |
| GO:0044464 | cell part | 0.017593004475606 |
| GO:0019199 | transmembrane receptor protein kinase activity | 0.0181262606177698 |
| GO:0016044 | membrane organization and biogenesis | 0.0181430825109875 |
| GO:0051179 | localization | 0.019163473646046 |
| GO:0042129 | regulation of T cell proliferation | 0.0193135347634839 |
| GO:0045113 | regulation of integrin biosynthetic process | 0.0193135347634839 |
| GO:0008321 | Ral guanyl-nucleotide exchange factor activity | 0.0193135347634839 |
| GO:0004925 | prolactin receptor activity | 0.0193135347634839 |
| GO:0001613 | A3 adenosine receptor activity, G-protein coupled | 0.0193135347634839 |
| GO:0042976 | activation of JAK protein | 0.0193135347634839 |
| GO:0042977 | tyrosine phosphorylation of JAK2 protein | 0.0193135347634839 |
| GO:0015235 | cobalamin transporter activity | 0.0193135347634839 |
| GO:0001887 | selenium metabolic process | 0.0193135347634839 |
| GO:0017047 | adrenocorticotropin-releasing hormone binding | 0.0193135347634839 |
| GO:0042978 | ornithine decarboxylase activator activity | 0.0193135347634839 |
| GO:0045112 | integrin biosynthetic process | 0.0193135347634839 |
| GO:0006817 | phosphate transport | 0.0196701894133717 |
| GO:0042330 | taxis | 0.0196701894133717 |
| GO:0006935 | chemotaxis | 0.0196701894133717 |
| GO:0042098 | T cell proliferation | 0.0210255164599685 |
| GO:0046649 | lymphocyte activation | 0.0233380060715598 |
| GO:0032944 | regulation of mononuclear cell proliferation | 0.0233380060715598 |
| GO:0050670 | regulation of lymphocyte proliferation | 0.0233380060715598 |
| GO:0051704 | multi-organism process | 0.0233380060715598 |
| GO:0001608 | nucleotide receptor activity, G-protein coupled | 0.0235260909069615 |
| GO:0045028 | purinergic nucleotide receptor activity, G-protein coupled | 0.0235260909069615 |
| GO:0016502 | nucleotide receptor activity | 0.0239970802093195 |
| GO:0001614 | purinergic nucleotide receptor activity | 0.0239970802093195 |
| GO:0006955 | immune response | 0.0267025298125823 |
| GO:0015808 | L-alanine transport | 0.0267025298125823 |
| GO:0015816 | glycine transport | 0.0267025298125823 |
| GO:0035238 | vitamin A biosynthetic process | 0.0267025298125823 |
| GO:0042362 | fat-soluble vitamin biosynthetic process | 0.0267025298125823 |
| GO:0045523 | interleukin-27 receptor binding | 0.0267025298125823 |
| GO:0005011 | macrophage colony stimulating factor receptor activity | 0.0267025298125823 |
| GO:0004996 | thyroid-stimulating hormone receptor activity | 0.0267025298125823 |
| GO:0032328 | alanine transport | 0.0267025298125823 |
| GO:0015193 | L-proline transmembrane transporter activity | 0.0267025298125823 |
| GO:0015180 | L-alanine transmembrane transporter activity | 0.0267025298125823 |
| GO:0032703 | negative regulation of interleukin-2 production | 0.0267025298125823 |
| GO:0042905 | 9-cis-retinoic acid metabolic process | 0.0267025298125823 |
| GO:0022858 | alanine transmembrane transporter activity | 0.0267025298125823 |
| GO:0004839 | ubiquitin activating enzyme activity | 0.0267025298125823 |
| GO:0042904 | 9-cis-retinoic acid biosynthetic process | 0.0267025298125823 |
| GO:0047035 | 3-alpha(17-beta)-hydroxysteroid dehydrogenase (NAD+) activity | 0.0267025298125823 |
| GO:0045321 | leukocyte activation | 0.0267025298125823 |
| GO:0032943 | mononuclear cell proliferation | 0.0276302758516279 |
| GO:0046651 | lymphocyte proliferation | 0.0276302758516279 |
| GO:0007275 | multicellular organismal development | 0.0314084254055507 |
| GO:0050863 | regulation of T cell activation | 0.0334159177759208 |
| GO:0006810 | transport | 0.0346048099817885 |
| GO:0007171 | transmembrane receptor protein tyrosine kinase activation (dimerization) | 0.0346048099817885 |
| GO:0046640 | regulation of alpha-beta T cell proliferation | 0.0346048099817885 |
| GO:0006824 | cobalt ion transport | 0.0346048099817885 |
| GO:0004944 | C5a anaphylatoxin receptor activity | 0.0346048099817885 |
| GO:0004032 | aldehyde reductase activity | 0.0346048099817885 |
| GO:0015824 | proline transport | 0.0346048099817885 |
| GO:0045651 | positive regulation of macrophage differentiation | 0.0346048099817885 |
| GO:0015087 | cobalt ion transmembrane transporter activity | 0.0346048099817885 |
| GO:0046641 | positive regulation of alpha-beta T cell proliferation | 0.0346048099817885 |
| GO:0046635 | positive regulation of alpha-beta T cell activation | 0.0346048099817885 |
| GO:0001775 | cell activation | 0.0347772329378079 |
| GO:0007169 | transmembrane receptor protein tyrosine kinase signaling pathway | 0.0349313275065516 |
| GO:0048856 | anatomical structure development | 0.0356538591948679 |
| GO:0004896 | hematopoietin/interferon-class (D200-domain) cytokine receptor activity | 0.0394749453533912 |
| GO:0005887 | integral to plasma membrane | 0.0403396127586432 |
| GO:0008285 | negative regulation of cell proliferation | 0.0403396127586432 |
| GO:0051234 | establishment of localization | 0.0403396127586432 |
| GO:0004521 | endoribonuclease activity | 0.0403396127586432 |
| GO:0031226 | intrinsic to plasma membrane | 0.0403396127586432 |
| GO:0005044 | scavenger receptor activity | 0.0403396127586432 |
| GO:0004942 | anaphylatoxin receptor activity | 0.0403396127586432 |
| GO:0043353 | enucleate erythrocyte differentiation | 0.0403396127586432 |
| GO:0046633 | alpha-beta T cell proliferation | 0.0403396127586432 |
| GO:0042448 | progesterone metabolic process | 0.0403396127586432 |
| GO:0015187 | glycine transmembrane transporter activity | 0.0403396127586432 |
| GO:0046634 | regulation of alpha-beta T cell activation | 0.0403396127586432 |
| GO:0006811 | ion transport | 0.0417672115495474 |
| GO:0007417 | central nervous system development | 0.0417672115495474 |
| GO:0051249 | regulation of lymphocyte activation | 0.04215284769159 |
| GO:0042127 | regulation of cell proliferation | 0.0444766695891267 |
| GO:0008283 | cell proliferation | 0.0444766695891267 |
| GO:0050865 | regulation of cell activation | 0.0444766695891267 |
| GO:0048518 | positive regulation of biological process | 0.0444766695891267 |
| GO:0007565 | female pregnancy | 0.0444766695891267 |
| GO:0030669 | clathrin-coated endocytic vesicle membrane | 0.0444766695891267 |
| GO:0030128 | clathrin coat of endocytic vesicle | 0.0444766695891267 |
| GO:0002763 | positive regulation of myeloid leukocyte differentiation | 0.0444766695891267 |
| GO:0015889 | cobalamin transport | 0.0444766695891267 |
| GO:0030122 | AP-2 adaptor complex | 0.0444766695891267 |
| GO:0031401 | positive regulation of protein modification process | 0.0444766695891267 |
| GO:0042573 | retinoic acid metabolic process | 0.0444766695891267 |
| GO:0045649 | regulation of macrophage differentiation | 0.0444766695891267 |
| GO:0009791 | post-embryonic development | 0.0444766695891267 |
| GO:0007165 | signal transduction | 0.0471348704335649 |
| GO:0015698 | inorganic anion transport | 0.0486611446296584 |
| GO:0042445 | hormone metabolic process | 0.0494865261413427 |
| GO:0006026 | aminoglycan catabolic process | 0.0495684743890466 |
| GO:0030666 | endocytic vesicle membrane | 0.0495684743890466 |
| GO:0032663 | regulation of interleukin-2 production | 0.0495684743890466 |
| GO:0042572 | retinol metabolic process | 0.0495684743890466 |
| GO:0015884 | folic acid transport | 0.0495684743890466 |
| GO:0004560 | alpha-L-fucosidase activity | 0.0495684743890466 |
| GO:0006027 | glycosaminoglycan catabolic process | 0.0495684743890466 |
| GO:0015928 | fucosidase activity | 0.0495684743890466 |
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 |
|---|---|---|
| granulocyte monocyte progenitor cell | 1.03e-19 | 71 |
| macrophage dendritic cell progenitor | 1.23e-18 | 65 |
| myeloid lineage restricted progenitor cell | 1.25e-18 | 70 |
| monopoietic cell | 2.56e-18 | 63 |
| monocyte | 2.56e-18 | 63 |
| monoblast | 2.56e-18 | 63 |
| promonocyte | 2.56e-18 | 63 |
| myeloid leukocyte | 1.77e-17 | 76 |
| CD14-positive, CD16-negative classical monocyte | 4.87e-16 | 42 |
| classical monocyte | 1.17e-12 | 45 |
| myeloid cell | 1.65e-12 | 112 |
| common myeloid progenitor | 1.65e-12 | 112 |
| endothelial cell | 3.26e-07 | 35 |
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) |
|---|---|
|
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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
No analysis results for this cluster
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
"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.
