Coexpression cluster:C30: Difference between revisions
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|ontology_enrichment_disease= | |ontology_enrichment_disease= | ||
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Revision as of 18:54, 8 August 2012
Full id: C30_thyroid_throat_mesothelioma_mucinous_trachea_chorionic_mesenchymal
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:0006590 | thyroid hormone generation | 1.92406476097948e-05 |
GO:0042403 | thyroid hormone metabolic process | 2.51527238888078e-05 |
GO:0004996 | thyroid-stimulating hormone receptor activity | 9.63933668456168e-05 |
GO:0006576 | biogenic amine metabolic process | 0.0035761503229389 |
GO:0042445 | hormone metabolic process | 0.00428121725059609 |
GO:0006575 | amino acid derivative metabolic process | 0.00428121725059609 |
GO:0016500 | protein-hormone receptor activity | 0.00944236073511168 |
GO:0005242 | inward rectifier potassium channel activity | 0.011016681141165 |
GO:0030955 | potassium ion binding | 0.011016681141165 |
GO:0048523 | negative regulation of cellular process | 0.0136545899590433 |
GO:0035270 | endocrine system development | 0.0136545899590433 |
GO:0048519 | negative regulation of biological process | 0.0143299363710696 |
GO:0042446 | hormone biosynthetic process | 0.0151956513679919 |
GO:0048732 | gland development | 0.0151956513679919 |
GO:0016564 | transcription repressor activity | 0.0151956513679919 |
GO:0032501 | multicellular organismal process | 0.0151956513679919 |
GO:0043416 | regulation of skeletal muscle regeneration | 0.0151956513679919 |
GO:0051149 | positive regulation of muscle cell differentiation | 0.0151956513679919 |
GO:0060022 | hard palate development | 0.0151956513679919 |
GO:0051155 | positive regulation of striated muscle cell differentiation | 0.0151956513679919 |
GO:0048712 | negative regulation of astrocyte differentiation | 0.0151956513679919 |
GO:0043415 | positive regulation of skeletal muscle regeneration | 0.0151956513679919 |
GO:0051153 | regulation of striated muscle cell differentiation | 0.0151956513679919 |
GO:0031420 | alkali metal ion binding | 0.0151956513679919 |
GO:0048522 | positive regulation of cellular process | 0.0183841735232803 |
GO:0031404 | chloride ion binding | 0.0183841735232803 |
GO:0043168 | anion binding | 0.0183841735232803 |
GO:0006813 | potassium ion transport | 0.0196232515339834 |
GO:0015111 | iodide transmembrane transporter activity | 0.0233802111284043 |
GO:0060023 | soft palate development | 0.0233802111284043 |
GO:0048518 | positive regulation of biological process | 0.0247550109457323 |
GO:0016481 | negative regulation of transcription | 0.0247550109457323 |
GO:0045934 | negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0284236746073842 |
GO:0014014 | negative regulation of gliogenesis | 0.0284236746073842 |
GO:0045686 | negative regulation of glial cell differentiation | 0.0284236746073842 |
GO:0048710 | regulation of astrocyte differentiation | 0.0284236746073842 |
GO:0060021 | palate development | 0.0284236746073842 |
GO:0007275 | multicellular organismal development | 0.0289537884802542 |
GO:0051179 | localization | 0.0304693755562727 |
GO:0055062 | phosphate ion homeostasis | 0.0311479303668775 |
GO:0043403 | skeletal muscle regeneration | 0.0311479303668775 |
GO:0030643 | cellular phosphate ion homeostasis | 0.0311479303668775 |
GO:0003835 | beta-galactoside alpha-2,6-sialyltransferase activity | 0.0311479303668775 |
GO:0051147 | regulation of muscle cell differentiation | 0.0311479303668775 |
GO:0060017 | parathyroid gland development | 0.0311479303668775 |
GO:0031324 | negative regulation of cellular metabolic process | 0.0357418220705116 |
GO:0030319 | cellular di-, tri-valent inorganic anion homeostasis | 0.0357418220705116 |
GO:0055061 | di-, tri-valent inorganic anion homeostasis | 0.0357418220705116 |
GO:0004800 | thyroxine 5'-deiodinase activity | 0.0357418220705116 |
GO:0006810 | transport | 0.0367338836742738 |
GO:0006451 | translational readthrough | 0.0367338836742738 |
GO:0055081 | anion homeostasis | 0.0367338836742738 |
GO:0001514 | selenocysteine incorporation | 0.0367338836742738 |
GO:0030002 | cellular anion homeostasis | 0.0367338836742738 |
GO:0000122 | negative regulation of transcription from RNA polymerase II promoter | 0.0367338836742738 |
GO:0050794 | regulation of cellular process | 0.0367338836742738 |
GO:0006357 | regulation of transcription from RNA polymerase II promoter | 0.0367338836742738 |
GO:0050954 | sensory perception of mechanical stimulus | 0.0367338836742738 |
GO:0007605 | sensory perception of sound | 0.0367338836742738 |
GO:0032502 | developmental process | 0.0367338836742738 |
GO:0051234 | establishment of localization | 0.0367338836742738 |
GO:0008143 | poly(A) binding | 0.0367338836742738 |
GO:0045685 | regulation of glial cell differentiation | 0.0367338836742738 |
GO:0014013 | regulation of gliogenesis | 0.0367338836742738 |
GO:0031069 | hair follicle morphogenesis | 0.0367338836742738 |
GO:0030878 | thyroid gland development | 0.0367338836742738 |
GO:0009892 | negative regulation of metabolic process | 0.0367338836742738 |
GO:0043565 | sequence-specific DNA binding | 0.0371370705448963 |
GO:0045595 | regulation of cell differentiation | 0.0399813981722057 |
GO:0048708 | astrocyte differentiation | 0.0399813981722057 |
GO:0042127 | regulation of cell proliferation | 0.0423628701472573 |
GO:0048562 | embryonic organ morphogenesis | 0.0485485001364824 |
GO:0005249 | voltage-gated potassium channel activity | 0.04917673850304 |
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><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) |
---|---|
{{{tfbs_overrepresentation_jaspar}}} |
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
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