Coexpression cluster:C19: Difference between revisions
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|ontology_enrichment_uberon= | |ontology_enrichment_uberon= | ||
|pathway_enrichment=0.000108536357284342;0.0238823869374849;4;92;Ribosome (KEGG):03010!0.000113186667950165;0.0238823869374849;4;93;Cytoplasmic Ribosomal Proteins (Wikipathways):WP477!0.00037879664527403;0.0479556552916922;2;11;Signaling by VEGF (Reactome):REACT_12529!0.000247996709377488;0.0392454792589875;4;114;Regulation of beta-cell development (Reactome):REACT_13698!4.08210231317272e-05;0.0238823869374849;5;143;Influenza Infection (Reactome):REACT_6167 | |pathway_enrichment=0.000108536357284342;0.0238823869374849;4;92;Ribosome (KEGG):03010!0.000113186667950165;0.0238823869374849;4;93;Cytoplasmic Ribosomal Proteins (Wikipathways):WP477!0.00037879664527403;0.0479556552916922;2;11;Signaling by VEGF (Reactome):REACT_12529!0.000247996709377488;0.0392454792589875;4;114;Regulation of beta-cell development (Reactome):REACT_13698!4.08210231317272e-05;0.0238823869374849;5;143;Influenza Infection (Reactome):REACT_6167 | ||
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}} | }} |
Revision as of 17:52, 8 August 2012
Full id: C19_embryonic_testis_cord_chronic_CD14_NK_mesothelioma
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
p.value | FDR | nGenes | nPathway | Name |
---|---|---|---|---|
0.000108536357284342 | 0.0238823869374849 | 4 | 92 | Ribosome (KEGG):03010 |
0.000113186667950165 | 0.0238823869374849 | 4 | 93 | Cytoplasmic Ribosomal Proteins (Wikipathways):WP477 |
0.00037879664527403 | 0.0479556552916922 | 2 | 11 | Signaling by VEGF (Reactome):REACT_12529 |
0.000247996709377488 | 0.0392454792589875 | 4 | 114 | Regulation of beta-cell development (Reactome):REACT_13698 |
4.08210231317272e-05 | 0.0238823869374849 | 5 | 143 | Influenza Infection (Reactome):REACT_6167 |
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:0044424 | intracellular part | 0.000118251118478727 |
GO:0044237 | cellular metabolic process | 0.000118251118478727 |
GO:0043229 | intracellular organelle | 0.000118251118478727 |
GO:0043226 | organelle | 0.000118251118478727 |
GO:0043231 | intracellular membrane-bound organelle | 0.000264921640815833 |
GO:0043227 | membrane-bound organelle | 0.000264921640815833 |
GO:0005634 | nucleus | 0.000264921640815833 |
GO:0043283 | biopolymer metabolic process | 0.000436316018510323 |
GO:0005622 | intracellular | 0.000454795999831926 |
GO:0003677 | DNA binding | 0.000638329673173698 |
GO:0003676 | nucleic acid binding | 0.000680990050141197 |
GO:0050789 | regulation of biological process | 0.000959069478515697 |
GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.00169134958778105 |
GO:0050794 | regulation of cellular process | 0.00222394499945679 |
GO:0044238 | primary metabolic process | 0.00261868380308172 |
GO:0019222 | regulation of metabolic process | 0.00261868380308172 |
GO:0010467 | gene expression | 0.00261868380308172 |
GO:0043170 | macromolecule metabolic process | 0.00288656026368036 |
GO:0031323 | regulation of cellular metabolic process | 0.00368743257469057 |
GO:0050930 | induction of positive chemotaxis | 0.00385761371356052 |
GO:0045449 | regulation of transcription | 0.00385761371356052 |
GO:0006355 | regulation of transcription, DNA-dependent | 0.00385761371356052 |
GO:0065007 | biological regulation | 0.00450793968205722 |
GO:0003723 | RNA binding | 0.00461241352901987 |
GO:0050926 | regulation of positive chemotaxis | 0.00461241352901987 |
GO:0050927 | positive regulation of positive chemotaxis | 0.00461241352901987 |
GO:0050918 | positive chemotaxis | 0.00461241352901987 |
GO:0006351 | transcription, DNA-dependent | 0.00461241352901987 |
GO:0032774 | RNA biosynthetic process | 0.00461241352901987 |
GO:0050921 | positive regulation of chemotaxis | 0.00507701195539429 |
GO:0048010 | vascular endothelial growth factor receptor signaling pathway | 0.00507701195539429 |
GO:0006350 | transcription | 0.00530438430267921 |
GO:0050920 | regulation of chemotaxis | 0.00532145601135416 |
GO:0004386 | helicase activity | 0.00532145601135416 |
GO:0010468 | regulation of gene expression | 0.00532145601135416 |
GO:0016070 | RNA metabolic process | 0.00532145601135416 |
GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.00532145601135416 |
GO:0005515 | protein binding | 0.00818749528637169 |
GO:0005830 | cytosolic ribosome (sensu Eukaryota) | 0.00902551579835063 |
GO:0044464 | cell part | 0.0111103756860159 |
GO:0048522 | positive regulation of cellular process | 0.0128505742145479 |
GO:0006512 | ubiquitin cycle | 0.0156105322851209 |
GO:0048518 | positive regulation of biological process | 0.024311547562387 |
GO:0032003 | interleukin-28 receptor binding | 0.0297058361788139 |
GO:0032023 | trypsinogen activation | 0.0297058361788139 |
GO:0045345 | positive regulation of MHC class I biosynthetic process | 0.0297058361788139 |
GO:0004595 | pantetheine-phosphate adenylyltransferase activity | 0.0297058361788139 |
GO:0004140 | dephospho-CoA kinase activity | 0.0297058361788139 |
GO:0005843 | cytosolic small ribosomal subunit (sensu Eukaryota) | 0.0317741409504344 |
GO:0045941 | positive regulation of transcription | 0.0369311487256354 |
GO:0045935 | positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0410791181765393 |
GO:0046475 | glycerophospholipid catabolic process | 0.0499800720172071 |
GO:0008106 | alcohol dehydrogenase (NADP+) activity | 0.0499800720172071 |
GO:0045343 | regulation of MHC class I biosynthetic process | 0.0499800720172071 |
GO:0045341 | MHC class I biosynthetic process | 0.0499800720172071 |
GO:0000281 | cytokinesis after mitosis | 0.0499800720172071 |
GO:0006931 | substrate-bound cell migration, cell attachment to substrate | 0.0499800720172071 |
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><br>disease_data<br>
Ontology term | p-value | n |
---|---|---|
hematopoietic stem cell | 8.58e-12 | 172 |
angioblastic mesenchymal cell | 8.58e-12 | 172 |
hematopoietic cell | 3.87e-11 | 182 |
hematopoietic oligopotent progenitor cell | 1.05e-10 | 165 |
hematopoietic multipotent progenitor cell | 1.05e-10 | 165 |
epithelial cell | 1.06e-08 | 254 |
classical monocyte | 5.43e-07 | 45 |
Ontology term | p-value | n |
---|---|---|
cancer | 4.46e-52 | 235 |
disease of cellular proliferation | 1.94e-51 | 239 |
cell type cancer | 1.77e-34 | 143 |
carcinoma | 3.20e-31 | 106 |
organ system cancer | 1.01e-23 | 137 |
hematologic cancer | 1.62e-15 | 51 |
immune system cancer | 1.62e-15 | 51 |
leukemia | 2.37e-11 | 39 |
myeloid leukemia | 1.04e-07 | 31 |
adenocarcinoma | 3.80e-07 | 25 |
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
"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.