Coexpression cluster:C1611: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
| (4 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
{ | |||
Latest revision as of 11:48, 17 September 2013
Full id: C1611_Renal_Hepatic_Eosinophils_Endothelial_CD14_heart_Neutrophils
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
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:0004696 | glycogen synthase kinase 3 activity | 0.00409951773641881 |
| GO:0046827 | positive regulation of protein export from nucleus | 0.00409951773641881 |
| GO:0010324 | membrane invagination | 0.00409951773641881 |
| GO:0006897 | endocytosis | 0.00409951773641881 |
| GO:0001849 | complement component C1q binding | 0.00445576494695808 |
| GO:0016044 | membrane organization and biogenesis | 0.00445576494695808 |
| GO:0001846 | opsonin binding | 0.00445576494695808 |
| GO:0046825 | regulation of protein export from nucleus | 0.00445576494695808 |
| GO:0002039 | p53 binding | 0.00445576494695808 |
| GO:0030877 | beta-catenin destruction complex | 0.00445576494695808 |
| GO:0050321 | tau-protein kinase activity | 0.00445576494695808 |
| GO:0006983 | ER overload response | 0.00445576494695808 |
| GO:0045192 | low-density lipoprotein catabolic process | 0.00445576494695808 |
| GO:0060070 | Wnt receptor signaling pathway through beta-catenin | 0.00517171777955849 |
| GO:0001848 | complement binding | 0.00543014381110518 |
| GO:0042159 | lipoprotein catabolic process | 0.00543014381110518 |
| GO:0042116 | macrophage activation | 0.0069243814818691 |
| GO:0046824 | positive regulation of nucleocytoplasmic transport | 0.0069243814818691 |
| GO:0018209 | peptidyl-serine modification | 0.0069243814818691 |
| GO:0018105 | peptidyl-serine phosphorylation | 0.0069243814818691 |
| GO:0016043 | cellular component organization and biogenesis | 0.0069243814818691 |
| GO:0016192 | vesicle-mediated transport | 0.0069243814818691 |
| GO:0051222 | positive regulation of protein transport | 0.0069243814818691 |
| GO:0006611 | protein export from nucleus | 0.00844490121160652 |
| GO:0033554 | cellular response to stress | 0.00926471749863026 |
| GO:0030169 | low-density lipoprotein binding | 0.00946487743275784 |
| GO:0051059 | NF-kappaB binding | 0.00965017914071661 |
| GO:0006810 | transport | 0.00980772946980233 |
| GO:0051234 | establishment of localization | 0.0101317931421153 |
| GO:0006984 | ER-nuclear signaling pathway | 0.0101317931421153 |
| GO:0051716 | cellular response to stimulus | 0.0110433382966838 |
| GO:0051179 | localization | 0.0110433382966838 |
| GO:0022610 | biological adhesion | 0.0110433382966838 |
| GO:0007155 | cell adhesion | 0.0110433382966838 |
| GO:0002274 | myeloid leukocyte activation | 0.0110433382966838 |
| GO:0051223 | regulation of protein transport | 0.0110433382966838 |
| GO:0046822 | regulation of nucleocytoplasmic transport | 0.0110433382966838 |
| GO:0008034 | lipoprotein binding | 0.0110433382966838 |
| GO:0051050 | positive regulation of transport | 0.0140958045221106 |
| GO:0006909 | phagocytosis | 0.0144654687403195 |
| GO:0006898 | receptor-mediated endocytosis | 0.0144654687403195 |
| GO:0006950 | response to stress | 0.0147825226066546 |
| GO:0051168 | nuclear export | 0.0148005673400166 |
| GO:0005977 | glycogen metabolic process | 0.0154266528202848 |
| GO:0006073 | glucan metabolic process | 0.0154266528202848 |
| GO:0006112 | energy reserve metabolic process | 0.0172885394330931 |
| GO:0042157 | lipoprotein metabolic process | 0.0252825281241136 |
| GO:0044264 | cellular polysaccharide metabolic process | 0.0252825281241136 |
| GO:0005976 | polysaccharide metabolic process | 0.0253547441008835 |
| GO:0007596 | blood coagulation | 0.0288789978975099 |
| GO:0050817 | coagulation | 0.0288789978975099 |
| GO:0007599 | hemostasis | 0.0291541032241128 |
| GO:0051049 | regulation of transport | 0.0299617073999914 |
| GO:0015980 | energy derivation by oxidation of organic compounds | 0.0312717550240248 |
| GO:0018193 | peptidyl-amino acid modification | 0.0317491159829751 |
| GO:0050878 | regulation of body fluid levels | 0.0322091855854129 |
| GO:0042060 | wound healing | 0.0331571654041858 |
| GO:0016055 | Wnt receptor signaling pathway | 0.0360530277052107 |
| GO:0006913 | nucleocytoplasmic transport | 0.0374829917162732 |
| GO:0051169 | nuclear transport | 0.0374829917162732 |
| GO:0045321 | leukocyte activation | 0.0425105027103473 |
| GO:0001775 | cell activation | 0.0484713101515121 |
| GO:0005515 | protein binding | 0.0484713101515121 |
| GO:0006605 | protein targeting | 0.0490166176015429 |
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>
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 | 0.737422 |
| MA0004.1 | 0.626788 |
| MA0006.1 | 0.452993 |
| MA0007.1 | 0.606704 |
| MA0009.1 | 1.11255 |
| MA0014.1 | 1.02528 |
| MA0017.1 | 0.496101 |
| MA0019.1 | 0.784036 |
| MA0024.1 | 1.00439 |
| MA0025.1 | 1.24931 |
| MA0027.1 | 2.73598 |
| MA0028.1 | 0.470679 |
| MA0029.1 | 1.02437 |
| MA0030.1 | 1.01252 |
| MA0031.1 | 0.945567 |
| MA0038.1 | 0.736268 |
| MA0040.1 | 1.03042 |
| MA0041.1 | 0.64667 |
| MA0042.1 | 0.612397 |
| MA0043.1 | 1.11288 |
| MA0046.1 | 1.10134 |
| MA0048.1 | 1.7027 |
| MA0050.1 | 0.613347 |
| MA0051.1 | 0.731787 |
| MA0052.1 | 1.03442 |
| MA0055.1 | 3.37159 |
| MA0056.1 | 0 |
| MA0057.1 | 1.66737 |
| MA0058.1 | 0.523638 |
| MA0059.1 | 0.522232 |
| MA0060.1 | 0.321781 |
| MA0061.1 | 0.791444 |
| MA0063.1 | 0 |
| MA0066.1 | 0.736721 |
| MA0067.1 | 1.43651 |
| MA0068.1 | 0.247962 |
| MA0069.1 | 1.09737 |
| MA0070.1 | 1.08584 |
| MA0071.1 | 0.695094 |
| MA0072.1 | 1.0812 |
| MA0073.1 | 0.215829 |
| MA0074.1 | 0.730989 |
| MA0076.1 | 1.33654 |
| MA0077.1 | 1.07324 |
| MA0078.1 | 0.836493 |
| MA0081.1 | 0.522409 |
| MA0083.1 | 1.12028 |
| MA0084.1 | 1.62584 |
| MA0087.1 | 1.07867 |
| MA0088.1 | 0.818263 |
| MA0089.1 | 0 |
| MA0090.1 | 0.556637 |
| MA0091.1 | 0.629594 |
| MA0092.1 | 0.588959 |
| MA0093.1 | 0.456342 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.750974 |
| MA0101.1 | 1.16366 |
| MA0103.1 | 0.442769 |
| MA0105.1 | 0.520776 |
| MA0106.1 | 0.779931 |
| MA0107.1 | 0.378225 |
| MA0108.2 | 0.94238 |
| MA0109.1 | 0 |
| MA0111.1 | 0.5713 |
| MA0113.1 | 1.8711 |
| MA0114.1 | 0.372523 |
| MA0115.1 | 1.35895 |
| MA0116.1 | 1.76306 |
| MA0117.1 | 1.1512 |
| MA0119.1 | 0.504689 |
| MA0122.1 | 1.17777 |
| MA0124.1 | 1.31673 |
| MA0125.1 | 1.23103 |
| MA0130.1 | 0 |
| MA0131.1 | 0.855546 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.14377 |
| MA0136.1 | 0.743749 |
| MA0139.1 | 0.277033 |
| MA0140.1 | 0.692258 |
| MA0141.1 | 0.520334 |
| MA0142.1 | 0.912455 |
| MA0143.1 | 0.797437 |
| MA0144.1 | 0.938075 |
| MA0145.1 | 0.442008 |
| MA0146.1 | 0.6031 |
| MA0147.1 | 0.386018 |
| MA0148.1 | 0.653474 |
| MA0149.1 | 2.7505 |
| MA0062.2 | 0.777733 |
| MA0035.2 | 0.691506 |
| MA0039.2 | 0.311551 |
| MA0138.2 | 0.837782 |
| MA0002.2 | 0.30855 |
| MA0137.2 | 0.47779 |
| MA0104.2 | 0.320919 |
| MA0047.2 | 0.767096 |
| MA0112.2 | 2.6393 |
| MA0065.2 | 0.146576 |
| MA0150.1 | 0.550239 |
| MA0151.1 | 0 |
| MA0152.1 | 0.69926 |
| MA0153.1 | 1.21379 |
| MA0154.1 | 0.98952 |
| MA0155.1 | 0.813062 |
| MA0156.1 | 0.480289 |
| MA0157.1 | 0.883854 |
| MA0158.1 | 0 |
| MA0159.1 | 1.00463 |
| MA0160.1 | 0.669748 |
| MA0161.1 | 0 |
| MA0162.1 | 0.81299 |
| MA0163.1 | 5.18163 |
| MA0164.1 | 0.810347 |
| MA0080.2 | 1.15604 |
| MA0018.2 | 0.781393 |
| MA0099.2 | 0.699641 |
| MA0079.2 | 3.15891 |
| MA0102.2 | 1.66336 |
| MA0258.1 | 0.914277 |
| MA0259.1 | 0.395396 |
| 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.
