Coexpression cluster:C105: Difference between revisions
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Latest revision as of 10:32, 17 September 2013
Full id: C105_heart_skeletal_occipital_hippocampus_acute_Sebocyte_penis
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:0005332 | gamma-aminobutyric acid:sodium symporter activity | 0.013582317476148 |
| GO:0015185 | L-gamma-aminobutyric acid transmembrane transporter activity | 0.013582317476148 |
| GO:0005283 | sodium:amino acid symporter activity | 0.013582317476148 |
| GO:0005416 | cation:amino acid symporter activity | 0.013582317476148 |
| GO:0005100 | Rho GTPase activator activity | 0.0183740213959862 |
| GO:0005275 | amine transmembrane transporter activity | 0.0183740213959862 |
| GO:0015179 | L-amino acid transmembrane transporter activity | 0.0183740213959862 |
| GO:0005343 | organic acid:sodium symporter activity | 0.0183740213959862 |
| GO:0005328 | neurotransmitter:sodium symporter activity | 0.0183740213959862 |
| GO:0030308 | negative regulation of cell growth | 0.0183740213959862 |
| GO:0005326 | neurotransmitter transporter activity | 0.0183740213959862 |
| GO:0045792 | negative regulation of cell size | 0.0183740213959862 |
| GO:0045926 | negative regulation of growth | 0.0183740213959862 |
| GO:0015171 | amino acid transmembrane transporter activity | 0.0183740213959862 |
| GO:0030155 | regulation of cell adhesion | 0.0183740213959862 |
| GO:0006836 | neurotransmitter transport | 0.0203539814997523 |
| GO:0015370 | solute:sodium symporter activity | 0.021609489514765 |
| GO:0046943 | carboxylic acid transmembrane transporter activity | 0.0217481310394723 |
| GO:0005342 | organic acid transmembrane transporter activity | 0.0217481310394723 |
| GO:0015294 | solute:cation symporter activity | 0.0237858771763283 |
| GO:0001558 | regulation of cell growth | 0.0312736747295867 |
| GO:0005099 | Ras GTPase activator activity | 0.0312736747295867 |
| GO:0016049 | cell growth | 0.0343385594509565 |
| GO:0040008 | regulation of growth | 0.0343385594509565 |
| GO:0008361 | regulation of cell size | 0.0343385594509565 |
| GO:0015293 | symporter activity | 0.0387673400410537 |
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><br>uberon_data<br>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| neural tube | 1.62e-18 | 56 |
| neural rod | 1.62e-18 | 56 |
| future spinal cord | 1.62e-18 | 56 |
| neural keel | 1.62e-18 | 56 |
| regional part of nervous system | 2.89e-17 | 53 |
| regional part of brain | 2.89e-17 | 53 |
| nervous system | 3.85e-16 | 89 |
| central nervous system | 9.40e-16 | 81 |
| brain | 5.29e-15 | 68 |
| future brain | 5.29e-15 | 68 |
| regional part of forebrain | 1.07e-14 | 41 |
| forebrain | 1.07e-14 | 41 |
| anterior neural tube | 1.07e-14 | 41 |
| future forebrain | 1.07e-14 | 41 |
| adult organism | 2.84e-14 | 114 |
| neurectoderm | 1.07e-13 | 86 |
| brain grey matter | 1.41e-12 | 34 |
| gray matter | 1.41e-12 | 34 |
| neural plate | 2.72e-12 | 82 |
| presumptive neural plate | 2.72e-12 | 82 |
| telencephalon | 1.37e-11 | 34 |
| regional part of telencephalon | 2.15e-11 | 32 |
| cerebral hemisphere | 5.77e-11 | 32 |
| ecto-epithelium | 1.83e-09 | 104 |
| regional part of cerebral cortex | 6.26e-09 | 22 |
| organ system subdivision | 8.36e-09 | 223 |
| ectoderm-derived structure | 8.96e-09 | 171 |
| ectoderm | 8.96e-09 | 171 |
| presumptive ectoderm | 8.96e-09 | 171 |
| pre-chordal neural plate | 6.47e-08 | 61 |
| cerebral cortex | 8.20e-08 | 25 |
| pallium | 8.20e-08 | 25 |
| neocortex | 9.54e-08 | 20 |
| neural nucleus | 9.74e-07 | 9 |
| nucleus of brain | 9.74e-07 | 9 |
| Ontology term | p-value | n |
|---|---|---|
| disease of cellular proliferation | 2.07e-25 | 239 |
| cancer | 6.83e-25 | 235 |
| cell type cancer | 1.07e-12 | 143 |
| organ system cancer | 7.96e-12 | 137 |
| carcinoma | 4.15e-08 | 106 |
| hematologic cancer | 3.63e-07 | 51 |
| immune system cancer | 3.63e-07 | 51 |
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 |
| MA0004.1 | 2.3934e-05 |
| MA0006.1 | 9.89923e-07 |
| MA0007.1 | 1.3995e-05 |
| MA0009.1 | 0.252275 |
| MA0014.1 | 0 |
| MA0017.1 | 3.65165e-07 |
| MA0019.1 | 0.000628636 |
| MA0024.1 | 0.00988067 |
| MA0025.1 | 0.056119 |
| MA0027.1 | 1.18893 |
| MA0028.1 | 1.28676e-07 |
| MA0029.1 | 0.0118495 |
| MA0030.1 | 0.0106504 |
| MA0031.1 | 0.00547833 |
| MA0038.1 | 0.000270609 |
| MA0040.1 | 0.0124978 |
| MA0041.1 | 3.94674e-05 |
| MA0042.1 | 1.63487e-05 |
| MA0043.1 | 0.0240536 |
| MA0046.1 | 0.0221119 |
| MA0048.1 | 4.82164e-17 |
| MA0050.1 | 1.6774e-05 |
| MA0051.1 | 0.00024856 |
| MA0052.1 | 0.0129401 |
| MA0055.1 | 0 |
| MA0056.1 | 0 |
| MA0057.1 | 1.21023e-14 |
| MA0058.1 | 1.02609e-06 |
| MA0059.1 | 9.75558e-07 |
| MA0060.1 | 2.51875e-11 |
| MA0061.1 | 5.49785e-11 |
| MA0063.1 | 0 |
| MA0066.1 | 0.000272925 |
| MA0067.1 | 0.129223 |
| MA0068.1 | 1.21328e-09 |
| MA0069.1 | 0.0214691 |
| MA0070.1 | 0.0874332 |
| MA0071.1 | 0.000118808 |
| MA0072.1 | 0.0189844 |
| MA0073.1 | 0 |
| MA0074.1 | 0.000244797 |
| MA0076.1 | 1.87499e-06 |
| MA0077.1 | 0.017839 |
| MA0078.1 | 0.00140868 |
| MA0081.1 | 9.81798e-07 |
| MA0083.1 | 0.0253592 |
| MA0084.1 | 0.235205 |
| MA0087.1 | 0.0186157 |
| MA0088.1 | 0 |
| MA0089.1 | 0 |
| MA0090.1 | 4.041e-05 |
| MA0091.1 | 2.57318e-05 |
| MA0092.1 | 8.46866e-06 |
| MA0093.1 | 6.85265e-08 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.000355029 |
| MA0101.1 | 8.06263e-08 |
| MA0103.1 | 6.33078e-07 |
| MA0105.1 | 0 |
| MA0106.1 | 0.000587227 |
| MA0107.1 | 2.41043e-08 |
| MA0108.2 | 0.00529252 |
| MA0109.1 | 0 |
| MA0111.1 | 4.99406e-06 |
| MA0113.1 | 0.000778799 |
| MA0114.1 | 8.20707e-10 |
| MA0115.1 | 0.094847 |
| MA0116.1 | 1.46638e-09 |
| MA0117.1 | 0.0313298 |
| MA0119.1 | 5.09191e-07 |
| MA0122.1 | 0.0371471 |
| MA0124.1 | 0.0785459 |
| MA0125.1 | 0.0508028 |
| MA0130.1 | 0 |
| MA0131.1 | 0.00183799 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.856989 |
| MA0136.1 | 0.000311127 |
| MA0139.1 | 5.69773e-13 |
| MA0140.1 | 0.000111852 |
| MA0141.1 | 9.10947e-07 |
| MA0142.1 | 0.00377456 |
| MA0143.1 | 0.00078111 |
| MA0144.1 | 2.95579e-10 |
| MA0145.1 | 0 |
| MA0146.1 | 0 |
| MA0147.1 | 1.84684e-09 |
| MA0148.1 | 4.65229e-05 |
| MA0149.1 | 8.94152e-05 |
| MA0062.2 | 1.18554e-12 |
| MA0035.2 | 0.000110067 |
| MA0039.2 | 0 |
| MA0138.2 | 0.00143489 |
| MA0002.2 | 2.92312e-09 |
| MA0137.2 | 1.73869e-07 |
| MA0104.2 | 2.35804e-11 |
| MA0047.2 | 0.000472165 |
| MA0112.2 | 0 |
| MA0065.2 | 0 |
| MA0150.1 | 2.55675e-06 |
| MA0151.1 | 0 |
| MA0152.1 | 0.000129708 |
| MA0153.1 | 0.0460864 |
| MA0154.1 | 0 |
| MA0155.1 | 0 |
| MA0156.1 | 1.92928e-07 |
| MA0157.1 | 0.0026644 |
| MA0158.1 | 0 |
| MA0159.1 | 1.92515e-09 |
| MA0160.1 | 6.8046e-05 |
| MA0161.1 | 0 |
| MA0162.1 | 0 |
| MA0163.1 | 0 |
| MA0164.1 | 0.00095582 |
| MA0080.2 | 6.88208e-08 |
| MA0018.2 | 0.000601703 |
| MA0099.2 | 0.000130745 |
| MA0079.2 | 0 |
| MA0102.2 | 0.259495 |
| MA0258.1 | 1.43431e-10 |
| MA0259.1 | 3.16559e-09 |
| 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
