Coexpression cluster:C954: Difference between revisions
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Latest revision as of 11:34, 17 September 2013
Full id: C954_heart_CD14_Neutrophils_Eosinophils_Lymphatic_renal_Monocytederived
Phase1 CAGE Peaks
| Hg19::chr6:160100686..160100698,- | p4@AK093984 |
| Hg19::chr6:160101581..160101593,- | p18@SOD2 |
| Hg19::chr6:160101609..160101626,- | p21@SOD2 |
| Hg19::chr6:160101648..160101695,- | p7@SOD2 |
| Hg19::chr6:160102006..160102195,- | p1@BC041951 |
| Hg19::chr6:160102208..160102232,- | p6@BC041951 |
| Hg19::chr6:160102300..160102326,- | p5@BC041951 |
| Hg19::chr6:160102610..160102627,- | p3@BC041951 |
| Hg19::chr6:160112805..160112821,- | p@chr6:160112805..160112821 - |
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:0008383 | manganese superoxide dismutase activity | 0.0027375485694101 |
| GO:0001315 | age-dependent response to reactive oxygen species | 0.0027375485694101 |
| GO:0000303 | response to superoxide | 0.00342193571176262 |
| GO:0000305 | response to oxygen radical | 0.00342193571176262 |
| GO:0016721 | oxidoreductase activity, acting on superoxide radicals as acceptor | 0.00410632285411515 |
| GO:0004784 | superoxide dismutase activity | 0.00410632285411515 |
| GO:0001836 | release of cytochrome c from mitochondria | 0.00508401877176161 |
| GO:0008637 | apoptotic mitochondrial changes | 0.00574885199576121 |
| GO:0042542 | response to hydrogen peroxide | 0.00574885199576121 |
| GO:0006801 | superoxide metabolic process | 0.00574885199576121 |
| GO:0000302 | response to reactive oxygen species | 0.00671943739764298 |
| GO:0006302 | double-strand break repair | 0.0082126457082303 |
| GO:0006800 | oxygen and reactive oxygen species metabolic process | 0.00947612966334266 |
| GO:0008632 | apoptotic program | 0.0162427881784999 |
| GO:0007005 | mitochondrion organization and biogenesis | 0.0162427881784999 |
| GO:0006979 | response to oxidative stress | 0.0205316142705758 |
| GO:0030145 | manganese ion binding | 0.0236717435119579 |
| GO:0031980 | mitochondrial lumen | 0.0263669151685289 |
| GO:0005759 | mitochondrial matrix | 0.0263669151685289 |
| GO:0043066 | negative regulation of apoptosis | 0.0299826748078249 |
| GO:0043069 | negative regulation of programmed cell death | 0.0299826748078249 |
| GO:0005743 | mitochondrial inner membrane | 0.0389478501011528 |
| GO:0019866 | organelle inner membrane | 0.0393968946293367 |
| GO:0006281 | DNA repair | 0.0438007771105616 |
| GO:0031966 | mitochondrial membrane | 0.0438007771105616 |
| GO:0006357 | regulation of transcription from RNA polymerase II promoter | 0.0438007771105616 |
| GO:0005740 | mitochondrial envelope | 0.0438007771105616 |
| GO:0006974 | response to DNA damage stimulus | 0.0438007771105616 |
| GO:0009719 | response to endogenous stimulus | 0.0486675301228462 |
| GO:0042981 | regulation of apoptosis | 0.0486675301228462 |
| GO:0043067 | regulation of programmed cell death | 0.0486675301228462 |
| GO:0044429 | mitochondrial part | 0.0486675301228462 |
| GO:0042221 | response to chemical stimulus | 0.0486675301228462 |
| GO:0031967 | organelle envelope | 0.0486675301228462 |
| GO:0031975 | envelope | 0.0486675301228462 |
| GO:0006366 | transcription from RNA polymerase II promoter | 0.0486675301228462 |
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 |
|---|---|---|
| defensive cell | 1.16e-25 | 48 |
| phagocyte | 1.16e-25 | 48 |
| classical monocyte | 3.83e-23 | 42 |
| CD14-positive, CD16-negative classical monocyte | 3.83e-23 | 42 |
| myeloid leukocyte | 1.82e-22 | 72 |
| monopoietic cell | 2.13e-21 | 59 |
| monocyte | 2.13e-21 | 59 |
| monoblast | 2.13e-21 | 59 |
| promonocyte | 2.13e-21 | 59 |
| macrophage dendritic cell progenitor | 3.92e-20 | 61 |
| myeloid lineage restricted progenitor cell | 2.45e-17 | 66 |
| granulocyte monocyte progenitor cell | 7.83e-17 | 67 |
| stuff accumulating cell | 1.20e-12 | 87 |
| myeloid cell | 4.50e-09 | 108 |
| common myeloid progenitor | 4.50e-09 | 108 |
| leukocyte | 3.87e-07 | 136 |
| nongranular leukocyte | 3.98e-07 | 115 |
| Ontology term | p-value | n |
|---|---|---|
| hemolymphoid system | 1.10e-16 | 108 |
| hematopoietic system | 1.67e-16 | 98 |
| blood island | 1.67e-16 | 98 |
| bone marrow | 1.12e-15 | 76 |
| immune system | 9.75e-14 | 93 |
| bone element | 2.57e-13 | 82 |
| musculoskeletal system | 3.46e-13 | 167 |
| skeletal element | 4.48e-13 | 90 |
| skeletal system | 4.55e-13 | 100 |
| adult organism | 8.53e-13 | 114 |
| mesoderm | 6.34e-09 | 315 |
| mesoderm-derived structure | 6.34e-09 | 315 |
| presumptive mesoderm | 6.34e-09 | 315 |
| lateral plate mesoderm | 4.56e-08 | 203 |
| anatomical system | 6.22e-07 | 624 |
| germ layer | 6.25e-07 | 560 |
| germ layer / neural crest | 6.25e-07 | 560 |
| embryonic tissue | 6.25e-07 | 560 |
| presumptive structure | 6.25e-07 | 560 |
| germ layer / neural crest derived structure | 6.25e-07 | 560 |
| epiblast (generic) | 6.25e-07 | 560 |
| anatomical group | 7.67e-07 | 625 |
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 | 0.000472949 |
| MA0004.1 | 1.06719 |
| MA0006.1 | 0.265592 |
| MA0007.1 | 0.397529 |
| MA0009.1 | 0.870971 |
| MA0014.1 | 0.00594475 |
| MA0017.1 | 0.815464 |
| MA0019.1 | 0.558663 |
| MA0024.1 | 0.766783 |
| MA0025.1 | 1.00397 |
| MA0027.1 | 2.48103 |
| MA0028.1 | 0.280275 |
| MA0029.1 | 0.785955 |
| MA0030.1 | 0.774581 |
| MA0031.1 | 0.710608 |
| MA0038.1 | 0.514558 |
| MA0040.1 | 0.791764 |
| MA0041.1 | 0.433167 |
| MA0042.1 | 0.402577 |
| MA0043.1 | 0.871285 |
| MA0046.1 | 0.860127 |
| MA0048.1 | 0.0764047 |
| MA0050.1 | 1.04113 |
| MA0051.1 | 0.510444 |
| MA0052.1 | 0.795605 |
| MA0055.1 | 0.0199484 |
| MA0056.1 | 0 |
| MA0057.1 | 0.0725989 |
| MA0058.1 | 1.56347 |
| MA0059.1 | 0.865474 |
| MA0060.1 | 0.488252 |
| MA0061.1 | 0.851955 |
| MA0063.1 | 0 |
| MA0066.1 | 0.514973 |
| MA0067.1 | 1.18766 |
| MA0068.1 | 0.109867 |
| MA0069.1 | 0.856287 |
| MA0070.1 | 0.845142 |
| MA0071.1 | 3.08738 |
| MA0072.1 | 1.96038 |
| MA0073.1 | 3.19635e-05 |
| MA0074.1 | 0.509711 |
| MA0076.1 | 0.339975 |
| MA0077.1 | 1.94461 |
| MA0078.1 | 0.607575 |
| MA0081.1 | 0.324031 |
| MA0083.1 | 0.878452 |
| MA0084.1 | 1.37471 |
| MA0087.1 | 1.95538 |
| MA0088.1 | 0.0408613 |
| MA0089.1 | 0 |
| MA0090.1 | 0.353576 |
| MA0091.1 | 0.417885 |
| MA0092.1 | 1.76221 |
| MA0093.1 | 0.73976 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.528088 |
| MA0101.1 | 0.746654 |
| MA0103.1 | 1.31682 |
| MA0105.1 | 0.854766 |
| MA0106.1 | 0.554855 |
| MA0107.1 | 1.75554 |
| MA0108.2 | 1.68573 |
| MA0109.1 | 0 |
| MA0111.1 | 1.70852 |
| MA0113.1 | 1.39997 |
| MA0114.1 | 0.582067 |
| MA0115.1 | 1.11137 |
| MA0116.1 | 0.208403 |
| MA0117.1 | 0.908433 |
| MA0119.1 | 0.83188 |
| MA0122.1 | 0.934245 |
| MA0124.1 | 1.06995 |
| MA0125.1 | 0.986127 |
| MA0130.1 | 0 |
| MA0131.1 | 0.625452 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.90122 |
| MA0136.1 | 0.521435 |
| MA0139.1 | 0.129876 |
| MA0140.1 | 0.474342 |
| MA0141.1 | 0.322254 |
| MA0142.1 | 0.679161 |
| MA0143.1 | 0.571113 |
| MA0144.1 | 0.1885 |
| MA0145.1 | 0.046841 |
| MA0146.1 | 0.0045741 |
| MA0147.1 | 0.607251 |
| MA0148.1 | 0.439278 |
| MA0149.1 | 0.464973 |
| MA0062.2 | 0.135498 |
| MA0035.2 | 3.07257 |
| MA0039.2 | 0.00489248 |
| MA0138.2 | 0.608783 |
| MA0002.2 | 0.152495 |
| MA0137.2 | 0.28622 |
| MA0104.2 | 0.161609 |
| MA0047.2 | 1.34084 |
| MA0112.2 | 0.0433683 |
| MA0065.2 | 0.182082 |
| MA0150.1 | 0.34802 |
| MA0151.1 | 0 |
| MA0152.1 | 1.20819 |
| MA0153.1 | 0.969315 |
| MA0154.1 | 0.225151 |
| MA0155.1 | 0.359913 |
| MA0156.1 | 0.288314 |
| MA0157.1 | 0.652111 |
| MA0158.1 | 0 |
| MA0159.1 | 0.212043 |
| MA0160.1 | 0.453945 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0107891 |
| MA0163.1 | 0.00648562 |
| MA0164.1 | 0.583138 |
| MA0080.2 | 0.268439 |
| MA0018.2 | 1.36887 |
| MA0099.2 | 0.481058 |
| MA0079.2 | 3.47892e-06 |
| MA0102.2 | 1.41188 |
| MA0258.1 | 0.180288 |
| MA0259.1 | 0.624802 |
| 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
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
This analysis result is provided for C0 - C305 clusters.
