Coexpression cluster:C1444
From FANTOM5_SSTAR
Full id: C1444_immature_migratory_CD14_amniotic_Eosinophils_CD19_Neutrophils
Phase1 CAGE Peaks
| Hg19::chr18:56338727..56338743,+ | p3@MALT1 |
| Hg19::chr1:11863148..11863162,- | p15@MTHFR |
| Hg19::chr1:11863171..11863195,- | p7@MTHFR |
| Hg19::chr2:65593835..65593877,- | p4@SPRED2 |
| Hg19::chr4:100737954..100738014,+ | p1@DAPP1 |
| Hg19::chr4:100738030..100738037,+ | p3@DAPP1 |
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 |
|---|---|---|---|---|
| 4.07274183298443e-05 | 0.0257804558027915 | 2 | 75 | B cell receptor signaling pathway (KEGG):04662 |
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:0019207 | kinase regulator activity | 0.00913554713606416 |
| GO:0045859 | regulation of protein kinase activity | 0.00913554713606416 |
| GO:0043549 | regulation of kinase activity | 0.00913554713606416 |
| GO:0051338 | regulation of transferase activity | 0.00913554713606416 |
| GO:0004489 | methylenetetrahydrofolate reductase (NADPH) activity | 0.00913554713606416 |
| GO:0032449 | CBM complex | 0.00913554713606416 |
| GO:0002711 | positive regulation of T cell mediated immunity | 0.00913554713606416 |
| GO:0032743 | positive regulation of interleukin-2 production | 0.00913554713606416 |
| GO:0002726 | positive regulation of T cell cytokine production | 0.00913554713606416 |
| GO:0002369 | T cell cytokine production | 0.00913554713606416 |
| GO:0002724 | regulation of T cell cytokine production | 0.00913554713606416 |
| GO:0002702 | positive regulation of production of molecular mediator of immune response | 0.00913554713606416 |
| GO:0002720 | positive regulation of cytokine production during immune response | 0.00913554713606416 |
| GO:0005173 | stem cell factor receptor binding | 0.00913554713606416 |
| GO:0002709 | regulation of T cell mediated immunity | 0.00913554713606416 |
| GO:0032663 | regulation of interleukin-2 production | 0.00913554713606416 |
| GO:0007243 | protein kinase cascade | 0.00913554713606416 |
| GO:0002824 | positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 0.00937218767921216 |
| GO:0002718 | regulation of cytokine production during immune response | 0.00937218767921216 |
| GO:0002821 | positive regulation of adaptive immune response | 0.00937218767921216 |
| GO:0002700 | regulation of production of molecular mediator of immune response | 0.00937218767921216 |
| GO:0002367 | cytokine production during immune response | 0.00937218767921216 |
| GO:0035014 | phosphoinositide 3-kinase regulator activity | 0.00937218767921216 |
| GO:0043621 | protein self-association | 0.00937218767921216 |
| GO:0002705 | positive regulation of leukocyte mediated immunity | 0.00937218767921216 |
| GO:0002456 | T cell mediated immunity | 0.00937218767921216 |
| GO:0002708 | positive regulation of lymphocyte mediated immunity | 0.00937218767921216 |
| GO:0002699 | positive regulation of immune effector process | 0.00967412384808736 |
| GO:0007250 | activation of NF-kappaB-inducing kinase | 0.00967412384808736 |
| GO:0002703 | regulation of leukocyte mediated immunity | 0.00967412384808736 |
| GO:0002706 | regulation of lymphocyte mediated immunity | 0.00967412384808736 |
| GO:0009086 | methionine biosynthetic process | 0.00967412384808736 |
| GO:0002819 | regulation of adaptive immune response | 0.00967412384808736 |
| GO:0002822 | regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. | 0.00967412384808736 |
| GO:0002697 | regulation of immune effector process | 0.0108425657983243 |
| GO:0050790 | regulation of catalytic activity | 0.0110794343074728 |
| GO:0009067 | aspartate family amino acid biosynthetic process | 0.0111055472779436 |
| GO:0050852 | T cell receptor signaling pathway | 0.0111055472779436 |
| GO:0006555 | methionine metabolic process | 0.0111055472779436 |
| GO:0019209 | kinase activator activity | 0.0111055472779436 |
| GO:0000188 | inactivation of MAPK activity | 0.0111055472779436 |
| GO:0065009 | regulation of a molecular function | 0.0114971521612877 |
| GO:0005942 | phosphoinositide 3-kinase complex | 0.0114971521612877 |
| GO:0000097 | sulfur amino acid biosynthetic process | 0.0114971521612877 |
| GO:0032623 | interleukin-2 production | 0.0118032216391385 |
| GO:0001819 | positive regulation of cytokine production | 0.0126451920081803 |
| GO:0043407 | negative regulation of MAP kinase activity | 0.0129136683529758 |
| GO:0002440 | production of molecular mediator of immune response | 0.0138461843222623 |
| GO:0050851 | antigen receptor-mediated signaling pathway | 0.0138461843222623 |
| GO:0009966 | regulation of signal transduction | 0.0138461843222623 |
| GO:0009066 | aspartate family amino acid metabolic process | 0.0138818511611803 |
| GO:0000096 | sulfur amino acid metabolic process | 0.0141005159226811 |
| GO:0002429 | immune response-activating cell surface receptor signaling pathway | 0.0143108870724969 |
| GO:0002768 | immune response-regulating cell surface receptor signaling pathway | 0.0145134253692679 |
| GO:0002757 | immune response-activating signal transduction | 0.0147085580619147 |
| GO:0002764 | immune response-regulating signal transduction | 0.014896681881578 |
| GO:0016646 | oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor | 0.0150781657186168 |
| GO:0050870 | positive regulation of T cell activation | 0.0175607085218321 |
| GO:0001817 | regulation of cytokine production | 0.0175607085218321 |
| GO:0005515 | protein binding | 0.0176817365756131 |
| GO:0051168 | nuclear export | 0.0180470171372814 |
| GO:0032501 | multicellular organismal process | 0.0180470171372814 |
| GO:0044272 | sulfur compound biosynthetic process | 0.0180470171372814 |
| GO:0030693 | caspase activity | 0.0197345665058968 |
| GO:0051251 | positive regulation of lymphocyte activation | 0.0198187015967892 |
| GO:0016645 | oxidoreductase activity, acting on the CH-NH group of donors | 0.019900253366686 |
| GO:0006469 | negative regulation of protein kinase activity | 0.0211674835851774 |
| GO:0033673 | negative regulation of kinase activity | 0.0211674835851774 |
| GO:0051348 | negative regulation of transferase activity | 0.021282316428579 |
| GO:0050863 | regulation of T cell activation | 0.021282316428579 |
| GO:0051259 | protein oligomerization | 0.0220465540844657 |
| GO:0032147 | activation of protein kinase activity | 0.0245368867182962 |
| GO:0002253 | activation of immune response | 0.0245454059728686 |
| GO:0002449 | lymphocyte mediated immunity | 0.0245536648911535 |
| GO:0002250 | adaptive immune response | 0.0249035740846093 |
| GO:0002460 | adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 0.0249035740846093 |
| GO:0051249 | regulation of lymphocyte activation | 0.0249035740846093 |
| GO:0002443 | leukocyte mediated immunity | 0.0252290237302291 |
| GO:0050865 | regulation of cell activation | 0.0255461214629594 |
| GO:0008652 | amino acid biosynthetic process | 0.0261196739881982 |
| GO:0050778 | positive regulation of immune response | 0.0261196739881982 |
| GO:0006790 | sulfur metabolic process | 0.0261196739881982 |
| GO:0002684 | positive regulation of immune system process | 0.0261196739881982 |
| GO:0043086 | negative regulation of catalytic activity | 0.0261196739881982 |
| GO:0043405 | regulation of MAP kinase activity | 0.027585235601085 |
| GO:0050776 | regulation of immune response | 0.0283196817116856 |
| GO:0042110 | T cell activation | 0.0283196817116856 |
| GO:0043123 | positive regulation of I-kappaB kinase/NF-kappaB cascade | 0.0283196817116856 |
| GO:0002682 | regulation of immune system process | 0.0283196817116856 |
| GO:0007165 | signal transduction | 0.0290757114283303 |
| GO:0051240 | positive regulation of multicellular organismal process | 0.0290757114283303 |
| GO:0043122 | regulation of I-kappaB kinase/NF-kappaB cascade | 0.0295774556148059 |
| GO:0002252 | immune effector process | 0.0297986264495236 |
| GO:0001816 | cytokine production | 0.0302816501657053 |
| GO:0009309 | amine biosynthetic process | 0.0315454828143631 |
| GO:0007154 | cell communication | 0.0344384781344397 |
| GO:0007249 | I-kappaB kinase/NF-kappaB cascade | 0.0360556320903252 |
| GO:0045860 | positive regulation of protein kinase activity | 0.0360849101192422 |
| GO:0004197 | cysteine-type endopeptidase activity | 0.0360849101192422 |
| GO:0033674 | positive regulation of kinase activity | 0.0362240154231583 |
| GO:0044271 | nitrogen compound biosynthetic process | 0.0362488046806512 |
| GO:0051347 | positive regulation of transferase activity | 0.0362488046806512 |
| GO:0000165 | MAPKKK cascade | 0.0365640539599067 |
| GO:0009967 | positive regulation of signal transduction | 0.0365640539599067 |
| GO:0006913 | nucleocytoplasmic transport | 0.0365640539599067 |
| GO:0046649 | lymphocyte activation | 0.0365640539599067 |
| GO:0051169 | nuclear transport | 0.0365640539599067 |
| GO:0007242 | intracellular signaling cascade | 0.0365640539599067 |
| GO:0008015 | blood circulation | 0.0365640539599067 |
| GO:0003013 | circulatory system process | 0.0365640539599067 |
| GO:0004842 | ubiquitin-protein ligase activity | 0.0371339497738497 |
| GO:0008639 | small protein conjugating enzyme activity | 0.037247914142536 |
| GO:0006916 | anti-apoptosis | 0.0378012012049799 |
| GO:0045321 | leukocyte activation | 0.0396561771719475 |
| GO:0044445 | cytosolic part | 0.0414769691378795 |
| GO:0043687 | post-translational protein modification | 0.0440000489858293 |
| GO:0001775 | cell activation | 0.0448071134385577 |
| GO:0004725 | protein tyrosine phosphatase activity | 0.0463221020896512 |
| GO:0043066 | negative regulation of apoptosis | 0.0478101264284914 |
| GO:0043069 | negative regulation of programmed cell death | 0.0480319249969728 |
| GO:0019787 | small conjugating protein ligase activity | 0.049888895594376 |
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 | 3.15e-22 | 98 |
| blood island | 3.15e-22 | 98 |
| bone marrow | 2.68e-18 | 76 |
| hemolymphoid system | 2.41e-17 | 108 |
| bone element | 3.82e-15 | 82 |
| immune system | 4.31e-15 | 93 |
| skeletal element | 6.10e-15 | 90 |
| skeletal system | 4.37e-13 | 100 |
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 | 0.515118 |
| MA0004.1 | 0.558729 |
| MA0006.1 | 1.01439 |
| MA0007.1 | 0.539222 |
| MA0009.1 | 1.03681 |
| MA0014.1 | 0.108006 |
| MA0017.1 | 0.432438 |
| MA0019.1 | 0.7124 |
| MA0024.1 | 0.929647 |
| MA0025.1 | 1.17262 |
| MA0027.1 | 2.65688 |
| MA0028.1 | 0.408079 |
| MA0029.1 | 0.949428 |
| MA0030.1 | 0.937696 |
| MA0031.1 | 0.871496 |
| MA0038.1 | 0.665566 |
| MA0040.1 | 0.955415 |
| MA0041.1 | 0.578072 |
| MA0042.1 | 0.544748 |
| MA0043.1 | 1.03713 |
| MA0046.1 | 1.02569 |
| MA0048.1 | 0.152639 |
| MA0050.1 | 1.34656 |
| MA0051.1 | 0.661179 |
| MA0052.1 | 0.959373 |
| MA0055.1 | 0.0586456 |
| MA0056.1 | 0 |
| MA0057.1 | 0.147053 |
| MA0058.1 | 0.458909 |
| MA0059.1 | 0.457555 |
| MA0060.1 | 0.267412 |
| MA0061.1 | 0.23892 |
| MA0063.1 | 0 |
| MA0066.1 | 0.66601 |
| MA0067.1 | 1.35893 |
| MA0068.1 | 0.199491 |
| MA0069.1 | 1.02175 |
| MA0070.1 | 1.01032 |
| MA0071.1 | 0.625297 |
| MA0072.1 | 1.00572 |
| MA0073.1 | 1.2326 |
| MA0074.1 | 0.660398 |
| MA0076.1 | 0.475586 |
| MA0077.1 | 0.997832 |
| MA0078.1 | 0.763954 |
| MA0081.1 | 1.15882 |
| MA0083.1 | 1.04447 |
| MA0084.1 | 1.5477 |
| MA0087.1 | 1.00322 |
| MA0088.1 | 1.09824 |
| MA0089.1 | 0 |
| MA0090.1 | 0.490736 |
| MA0091.1 | 1.37996 |
| MA0092.1 | 0.522012 |
| MA0093.1 | 0.394379 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 1.62836 |
| MA0101.1 | 0.397846 |
| MA0103.1 | 0.993014 |
| MA0105.1 | 0.134725 |
| MA0106.1 | 0.70837 |
| MA0107.1 | 0.320267 |
| MA0108.2 | 0.868347 |
| MA0109.1 | 0 |
| MA0111.1 | 0.504913 |
| MA0113.1 | 0.725375 |
| MA0114.1 | 0.314898 |
| MA0115.1 | 1.28169 |
| MA0116.1 | 0.323925 |
| MA0117.1 | 1.07516 |
| MA0119.1 | 1.12205 |
| MA0122.1 | 1.10154 |
| MA0124.1 | 1.23968 |
| MA0125.1 | 1.15445 |
| MA0130.1 | 0 |
| MA0131.1 | 0.782708 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.06778 |
| MA0136.1 | 1.61362 |
| MA0139.1 | 0.226048 |
| MA0140.1 | 0.622527 |
| MA0141.1 | 0.455728 |
| MA0142.1 | 0.838805 |
| MA0143.1 | 0.725558 |
| MA0144.1 | 0.299851 |
| MA0145.1 | 1.16614 |
| MA0146.1 | 0.718193 |
| MA0147.1 | 0.327615 |
| MA0148.1 | 0.584698 |
| MA0149.1 | 0.612449 |
| MA0062.2 | 0.23336 |
| MA0035.2 | 0.621793 |
| MA0039.2 | 1.86512 |
| MA0138.2 | 0.765223 |
| MA0002.2 | 0.255126 |
| MA0137.2 | 0.414885 |
| MA0104.2 | 0.26661 |
| MA0047.2 | 0.695777 |
| MA0112.2 | 3.64053 |
| MA0065.2 | 0.718489 |
| MA0150.1 | 2.10974 |
| MA0151.1 | 0 |
| MA0152.1 | 0.629368 |
| MA0153.1 | 1.13732 |
| MA0154.1 | 0.132326 |
| MA0155.1 | 0.318517 |
| MA0156.1 | 1.07131 |
| MA0157.1 | 0.810597 |
| MA0158.1 | 0 |
| MA0159.1 | 0.328286 |
| MA0160.1 | 0.600559 |
| MA0161.1 | 0 |
| MA0162.1 | 0.347838 |
| MA0163.1 | 0.273773 |
| MA0164.1 | 0.738243 |
| MA0080.2 | 1.80563 |
| MA0018.2 | 0.709805 |
| MA0099.2 | 0.629739 |
| MA0079.2 | 0.476723 |
| MA0102.2 | 1.58513 |
| MA0258.1 | 1.43672 |
| MA0259.1 | 0.336472 |
| 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 |
|---|---|---|---|---|
| POLR2A#5430 | 6 | 2.14745317655807 | 0.0101957067681878 | 0.0380309803622546 |
| SRF#6722 | 5 | 11.4976485518065 | 1.12681431027194e-05 | 0.000288157100270546 |
| TCF12#6938 | 3 | 5.31723245109321 | 0.01336734573386 | 0.0472476046127861 |
| TFAP2C#7022 | 3 | 5.40461430493011 | 0.0127757616669587 | 0.0460639291837155 |
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.
