Coexpression cluster:C2650: Difference between revisions
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Latest revision as of 12:10, 17 September 2013
Full id: C2650_Neural_hippocampus_amygdala_parietal_middle_medial_caudate
Phase1 CAGE Peaks
| Hg19::chr22:50523729..50523747,- | p3@MLC1 |
| Hg19::chr4:114214125..114214151,+ | p11@ANK2 |
| Hg19::chr5:16741975..16741994,- | p8@MYO10 |
| Hg19::chr5:36606700..36606729,+ | p1@SLC1A3 |
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:0015629 | actin cytoskeleton | 0.0178981509968156 |
| GO:0005313 | L-glutamate transmembrane transporter activity | 0.0178981509968156 |
| GO:0001504 | neurotransmitter uptake | 0.0178981509968156 |
| GO:0000299 | integral to membrane of membrane fraction | 0.0178981509968156 |
| GO:0015172 | acidic amino acid transmembrane transporter activity | 0.0178981509968156 |
| GO:0015813 | L-glutamate transport | 0.0178981509968156 |
| GO:0015800 | acidic amino acid transport | 0.0178981509968156 |
| GO:0017153 | sodium:dicarboxylate symporter activity | 0.0178981509968156 |
| GO:0005310 | dicarboxylic acid transmembrane transporter activity | 0.0178981509968156 |
| GO:0006835 | dicarboxylic acid transport | 0.0178981509968156 |
| GO:0005624 | membrane fraction | 0.0178981509968156 |
| GO:0043232 | intracellular non-membrane-bound organelle | 0.0178981509968156 |
| GO:0043228 | non-membrane-bound organelle | 0.0178981509968156 |
| GO:0015179 | L-amino acid transmembrane transporter activity | 0.0263385807155217 |
| GO:0000267 | cell fraction | 0.0264272426077618 |
| GO:0005343 | organic acid:sodium symporter activity | 0.0264272426077618 |
| GO:0015296 | anion:cation symporter activity | 0.0264272426077618 |
| GO:0015171 | amino acid transmembrane transporter activity | 0.0366909263885831 |
| GO:0006865 | amino acid transport | 0.0366909263885831 |
| GO:0015075 | ion transmembrane transporter activity | 0.0366909263885831 |
| GO:0006836 | neurotransmitter transport | 0.0366909263885831 |
| GO:0001505 | regulation of neurotransmitter levels | 0.0366909263885831 |
| GO:0015837 | amine transport | 0.0366909263885831 |
| GO:0005856 | cytoskeleton | 0.0366909263885831 |
| GO:0005200 | structural constituent of cytoskeleton | 0.0366909263885831 |
| GO:0015370 | solute:sodium symporter activity | 0.0366909263885831 |
| GO:0022891 | substrate-specific transmembrane transporter activity | 0.0366909263885831 |
| GO:0046943 | carboxylic acid transmembrane transporter activity | 0.0366909263885831 |
| GO:0046942 | carboxylic acid transport | 0.0366909263885831 |
| GO:0015849 | organic acid transport | 0.0366909263885831 |
| GO:0005342 | organic acid transmembrane transporter activity | 0.0366909263885831 |
| GO:0016459 | myosin complex | 0.0384030294254836 |
| GO:0022857 | transmembrane transporter activity | 0.0384966829879713 |
| GO:0015294 | solute:cation symporter activity | 0.0384966829879713 |
| GO:0022892 | substrate-specific transporter activity | 0.0418601036548849 |
| GO:0007154 | cell communication | 0.0418601036548849 |
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 |
|---|---|---|
| neuronal stem cell | 9.51e-10 | 8 |
| neural cell | 2.85e-08 | 25 |
| neuron | 4.72e-07 | 6 |
| neuroblast | 4.72e-07 | 6 |
| electrically signaling cell | 4.72e-07 | 6 |
| oligodendrocyte | 9.79e-07 | 7 |
| macroglial cell | 9.79e-07 | 7 |
| astrocyte | 9.79e-07 | 7 |
| oligodendrocyte precursor cell | 9.79e-07 | 7 |
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 | 0.0214529 |
| MA0004.1 | 0.71247 |
| MA0006.1 | 0.532262 |
| MA0007.1 | 0.6918 |
| MA0009.1 | 1.20602 |
| MA0014.1 | 0.0695829 |
| MA0017.1 | 0.577281 |
| MA0019.1 | 0.873355 |
| MA0024.1 | 1.09684 |
| MA0025.1 | 1.34373 |
| MA0027.1 | 2.83281 |
| MA0028.1 | 0.550763 |
| MA0029.1 | 1.11704 |
| MA0030.1 | 1.10506 |
| MA0031.1 | 1.03735 |
| MA0038.1 | 0.824639 |
| MA0040.1 | 1.12314 |
| MA0041.1 | 0.732902 |
| MA0042.1 | 0.697662 |
| MA0043.1 | 1.20635 |
| MA0046.1 | 1.19471 |
| MA0048.1 | 0.25531 |
| MA0050.1 | 0.69864 |
| MA0051.1 | 0.820063 |
| MA0052.1 | 1.12718 |
| MA0055.1 | 0.125954 |
| MA0056.1 | 0 |
| MA0057.1 | 0.69331 |
| MA0058.1 | 0.605914 |
| MA0059.1 | 0.604454 |
| MA0060.1 | 0.393285 |
| MA0061.1 | 0.946082 |
| MA0063.1 | 0 |
| MA0066.1 | 0.825101 |
| MA0067.1 | 1.53181 |
| MA0068.1 | 0.313194 |
| MA0069.1 | 1.19071 |
| MA0070.1 | 1.17908 |
| MA0071.1 | 0.782546 |
| MA0072.1 | 1.1744 |
| MA0073.1 | 0.00636811 |
| MA0074.1 | 0.819248 |
| MA0076.1 | 0.623864 |
| MA0077.1 | 1.16637 |
| MA0078.1 | 0.926725 |
| MA0081.1 | 0.604638 |
| MA0083.1 | 1.21381 |
| MA0084.1 | 1.72172 |
| MA0087.1 | 1.17185 |
| MA0088.1 | 1.02755 |
| MA0089.1 | 0 |
| MA0090.1 | 0.640115 |
| MA0091.1 | 0.715356 |
| MA0092.1 | 0.673508 |
| MA0093.1 | 0.535768 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.83965 |
| MA0101.1 | 0.539569 |
| MA0103.1 | 0.521546 |
| MA0105.1 | 1.22348 |
| MA0106.1 | 0.869173 |
| MA0107.1 | 1.1497 |
| MA0108.2 | 1.03412 |
| MA0109.1 | 0 |
| MA0111.1 | 0.655276 |
| MA0113.1 | 0.886811 |
| MA0114.1 | 0.447443 |
| MA0115.1 | 1.45393 |
| MA0116.1 | 0.457606 |
| MA0117.1 | 1.24497 |
| MA0119.1 | 0.586221 |
| MA0122.1 | 1.27173 |
| MA0124.1 | 1.41151 |
| MA0125.1 | 1.32534 |
| MA0130.1 | 0 |
| MA0131.1 | 0.94608 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.23748 |
| MA0136.1 | 0.832277 |
| MA0139.1 | 0.344952 |
| MA0140.1 | 0.779643 |
| MA0141.1 | 0.602484 |
| MA0142.1 | 1.00381 |
| MA0143.1 | 2.05538 |
| MA0144.1 | 0.430413 |
| MA0145.1 | 0.195821 |
| MA0146.1 | 0.061409 |
| MA0147.1 | 0.46175 |
| MA0148.1 | 0.739888 |
| MA0149.1 | 0.769072 |
| MA0062.2 | 0.353589 |
| MA0035.2 | 0.778873 |
| MA0039.2 | 0.0247757 |
| MA0138.2 | 0.928035 |
| MA0002.2 | 0.379056 |
| MA0137.2 | 0.558189 |
| MA0104.2 | 0.392359 |
| MA0047.2 | 0.856092 |
| MA0112.2 | 0.187982 |
| MA0065.2 | 0.199162 |
| MA0150.1 | 0.633493 |
| MA0151.1 | 0 |
| MA0152.1 | 0.78681 |
| MA0153.1 | 1.30799 |
| MA0154.1 | 0.229241 |
| MA0155.1 | 0.180766 |
| MA0156.1 | 0.560797 |
| MA0157.1 | 0.97481 |
| MA0158.1 | 0 |
| MA0159.1 | 0.462502 |
| MA0160.1 | 0.756582 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0928415 |
| MA0163.1 | 0.0725493 |
| MA0164.1 | 0.90014 |
| MA0080.2 | 0.535868 |
| MA0018.2 | 0.870662 |
| MA0099.2 | 0.7872 |
| MA0079.2 | 0.0626799 |
| MA0102.2 | 1.75932 |
| MA0258.1 | 0.418966 |
| MA0259.1 | 0.471671 |
| 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 |
|---|---|---|---|---|
| POU5F1#5460 | 1 | 83.8598003629764 | 0.0118715423909156 | 0.0432410984467908 |
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.
