MCL coexpression mm9:3596: Difference between revisions
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{{MCL_coexpression_mm9 | 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Latest revision as of 20:21, 17 September 2013
Phase1 CAGE Peaks
Short description | |
---|---|
Mm9::chr7:133935999..133936053,- | p1@Ppp4c |
Mm9::chr8:87550750..87550798,+ | p1@2310036O22Rik |
Mm9::chr9:110558998..110559048,+ | p1@Ccdc12 |
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
GO ID | GO name | FDR corrected p-value |
---|---|---|
GO:0004704 | NF-kappaB-inducing kinase activity | 0.00361584397085411 |
GO:0004722 | protein serine/threonine phosphatase activity | 0.0277214704432148 |
GO:0004702 | receptor signaling protein serine/threonine kinase activity | 0.0277214704432148 |
GO:0005057 | receptor signaling protein activity | 0.0388703226866816 |
GO:0030145 | manganese ion binding | 0.0433901276502493 |
GO:0004721 | phosphoprotein phosphatase activity | 0.0433901276502493 |
Relative expression of the co-expression cluster over median <br>Analyst:
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 |
---|---|---|
somatic cell | 1.23e-26 | 118 |
animal cell | 1.85e-24 | 115 |
eukaryotic cell | 1.85e-24 | 115 |
stem cell | 2.28e-16 | 97 |
motile cell | 5.12e-16 | 54 |
somatic stem cell | 1.54e-15 | 91 |
multi fate stem cell | 1.54e-15 | 91 |
connective tissue cell | 7.14e-15 | 46 |
mesenchymal cell | 7.14e-15 | 46 |
hematopoietic cell | 1.21e-13 | 32 |
hematopoietic oligopotent progenitor cell | 1.21e-13 | 32 |
hematopoietic stem cell | 1.21e-13 | 32 |
angioblastic mesenchymal cell | 1.21e-13 | 32 |
hematopoietic multipotent progenitor cell | 1.21e-13 | 32 |
hematopoietic lineage restricted progenitor cell | 2.44e-11 | 25 |
endo-epithelial cell | 2.18e-09 | 15 |
epithelial cell | 9.73e-09 | 25 |
common myeloid progenitor | 1.07e-08 | 19 |
leukocyte | 8.43e-08 | 17 |
nongranular leukocyte | 8.43e-08 | 17 |
myeloid cell | 2.10e-07 | 16 |
embryonic cell | 3.05e-07 | 70 |
nucleate cell | 7.20e-07 | 16 |
endodermal cell | 8.63e-07 | 20 |
Ontology term | p-value | n |
---|---|---|
hemolymphoid system | 2.42e-15 | 48 |
immune system | 2.42e-15 | 48 |
hematopoietic system | 4.32e-15 | 45 |
blood island | 4.32e-15 | 45 |
connective tissue | 7.14e-15 | 46 |
mucosa | 5.86e-09 | 15 |
bone marrow | 1.64e-08 | 16 |
intestinal mucosa | 4.21e-08 | 13 |
anatomical wall | 4.21e-08 | 13 |
wall of intestine | 4.21e-08 | 13 |
gastrointestinal system mucosa | 4.21e-08 | 13 |
segment of respiratory tract | 5.13e-08 | 27 |
hemopoietic organ | 6.90e-08 | 29 |
immune organ | 6.90e-08 | 29 |
thymus | 2.32e-07 | 23 |
neck | 2.32e-07 | 23 |
respiratory system epithelium | 2.32e-07 | 23 |
hemolymphoid system gland | 2.32e-07 | 23 |
pharyngeal epithelium | 2.32e-07 | 23 |
thymic region | 2.32e-07 | 23 |
pharyngeal gland | 2.32e-07 | 23 |
entire pharyngeal arch endoderm | 2.32e-07 | 23 |
thymus primordium | 2.32e-07 | 23 |
early pharyngeal endoderm | 2.32e-07 | 23 |
organ component layer | 6.31e-07 | 24 |
gland of gut | 7.00e-07 | 24 |
TFBS overrepresentation<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 | 0.899234 |
MA0004.1 | 0.801718 |
MA0006.1 | 0.60285 |
MA0007.1 | 0.784593 |
MA0009.1 | 1.27673 |
MA0014.1 | 0.133574 |
MA0017.1 | 0.635031 |
MA0019.1 | 1.08369 |
MA0024.1 | 1.23079 |
MA0025.1 | 1.51835 |
MA0027.1 | 2.9431 |
MA0028.1 | 2.53785 |
MA0029.1 | 1.20789 |
MA0030.1 | 1.21482 |
MA0031.1 | 1.17722 |
MA0038.1 | 0.963265 |
MA0040.1 | 1.28983 |
MA0041.1 | 0.714279 |
MA0042.1 | 0.69885 |
MA0043.1 | 1.3775 |
MA0046.1 | 1.31428 |
MA0048.1 | 0.353763 |
MA0050.1 | 0.845669 |
MA0051.1 | 0.973068 |
MA0052.1 | 1.29825 |
MA0055.1 | 1.06076 |
MA0056.1 | 0 |
MA0057.1 | 0.337566 |
MA0058.1 | 0.690848 |
MA0059.1 | 0.705317 |
MA0060.1 | 0.502699 |
MA0061.1 | 0.5406 |
MA0063.1 | 0 |
MA0066.1 | 0.951196 |
MA0067.1 | 1.63197 |
MA0068.1 | 0.343188 |
MA0069.1 | 1.29861 |
MA0070.1 | 1.28847 |
MA0071.1 | 0.844726 |
MA0072.1 | 1.2796 |
MA0073.1 | 0.0430758 |
MA0074.1 | 0.911576 |
MA0076.1 | 3.88666 |
MA0077.1 | 1.2569 |
MA0078.1 | 1.0091 |
MA0081.1 | 0.732313 |
MA0083.1 | 1.37668 |
MA0084.1 | 1.96428 |
MA0087.1 | 1.33189 |
MA0088.1 | 0.27999 |
MA0089.1 | 0 |
MA0090.1 | 0.762482 |
MA0091.1 | 0.816659 |
MA0092.1 | 0.762845 |
MA0093.1 | 0.62555 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.89873 |
MA0101.1 | 0.71579 |
MA0103.1 | 0.647985 |
MA0105.1 | 0.405648 |
MA0106.1 | 1.01755 |
MA0107.1 | 0.640607 |
MA0108.2 | 1.10817 |
MA0109.1 | 0 |
MA0111.1 | 0.778753 |
MA0113.1 | 0.986839 |
MA0114.1 | 0.537669 |
MA0115.1 | 1.38041 |
MA0116.1 | 0.602598 |
MA0117.1 | 1.34691 |
MA0119.1 | 0.716476 |
MA0122.1 | 1.36752 |
MA0124.1 | 1.57762 |
MA0125.1 | 1.5017 |
MA0130.1 | 0 |
MA0131.1 | 1.07881 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 1.4152 |
MA0136.1 | 0.933582 |
MA0139.1 | 1.16863 |
MA0140.1 | 0.898603 |
MA0141.1 | 0.671467 |
MA0142.1 | 1.16183 |
MA0143.1 | 1.00467 |
MA0144.1 | 0.541532 |
MA0145.1 | 0.794492 |
MA0146.1 | 0.151124 |
MA0147.1 | 0.556853 |
MA0148.1 | 0.820161 |
MA0149.1 | 0.722227 |
MA0062.2 | 3.80965 |
MA0035.2 | 0.903829 |
MA0039.2 | 0.40695 |
MA0138.2 | 1.07027 |
MA0002.2 | 0.466067 |
MA0137.2 | 0.668025 |
MA0104.2 | 0.48458 |
MA0047.2 | 0.962424 |
MA0112.2 | 0.29236 |
MA0065.2 | 0.292912 |
MA0150.1 | 0.784464 |
MA0151.1 | 0 |
MA0152.1 | 0.962542 |
MA0153.1 | 1.43238 |
MA0154.1 | 0.35067 |
MA0155.1 | 0.312898 |
MA0156.1 | 1.58027 |
MA0157.1 | 1.12772 |
MA0158.1 | 0 |
MA0159.1 | 0.569393 |
MA0160.1 | 0.823568 |
MA0161.1 | 0 |
MA0162.1 | 0.166722 |
MA0163.1 | 1.48428 |
MA0164.1 | 0.933981 |
MA0080.2 | 0.64167 |
MA0018.2 | 0.944669 |
MA0099.2 | 1.06348 |
MA0079.2 | 0.0332569 |
MA0102.2 | 2.01714 |
MA0258.1 | 0.520639 |
MA0259.1 | 0.543506 |
MA0442.1 | 0 |