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Coexpression cluster:C2600: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2600_Dendritic_xeroderma_Smooth_gall_B_CD14_plasma
|full_id=C2600_Dendritic_xeroderma_Smooth_gall_B_CD14_plasma
|gostat_on_coexpression_clusters=GO:0009615!response to virus!0.0467885317320146!4599$GO:0051707!response to other organism!0.0467885317320146!4599$GO:0006917!induction of apoptosis!0.0467885317320146!4599$GO:0012502!induction of programmed cell death!0.0467885317320146!4599$GO:0043065!positive regulation of apoptosis!0.0467885317320146!4599$GO:0043068!positive regulation of programmed cell death!0.0467885317320146!4599$GO:0003924!GTPase activity!0.0467885317320146!4599$GO:0009607!response to biotic stimulus!0.0467885317320146!4599$GO:0051704!multi-organism process!0.0479218179677381!4599
|gostat_on_coexpression_clusters=GO:0009615!response to virus!0.0467885317320146!4599$GO:0051707!response to other organism!0.0467885317320146!4599$GO:0006917!induction of apoptosis!0.0467885317320146!4599$GO:0012502!induction of programmed cell death!0.0467885317320146!4599$GO:0043065!positive regulation of apoptosis!0.0467885317320146!4599$GO:0043068!positive regulation of programmed cell death!0.0467885317320146!4599$GO:0003924!GTPase activity!0.0467885317320146!4599$GO:0009607!response to biotic stimulus!0.0467885317320146!4599$GO:0051704!multi-organism process!0.0479218179677381!4599

Revision as of 15:21, 12 September 2012


Full id: C2600_Dendritic_xeroderma_Smooth_gall_B_CD14_plasma



Phase1 CAGE Peaks

Hg19::chr1:79086118..79086182,+p1@IFI44L
Hg19::chr1:79101668..79101671,+p@chr1:79101668..79101671
+
Hg19::chr21:42798095..42798112,+p3@MX1
Hg19::chr21:42798124..42798146,+p2@MX1


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 IDGO nameFDR corrected p-value
GO:0009615response to virus0.0467885317320146
GO:0051707response to other organism0.0467885317320146
GO:0006917induction of apoptosis0.0467885317320146
GO:0012502induction of programmed cell death0.0467885317320146
GO:0043065positive regulation of apoptosis0.0467885317320146
GO:0043068positive regulation of programmed cell death0.0467885317320146
GO:0003924GTPase activity0.0467885317320146
GO:0009607response to biotic stimulus0.0467885317320146
GO:0051704multi-organism process0.0479218179677381



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>


Cell Type
Ontology termp-valuen
leukocyte6.82e-24140
nongranular leukocyte2.16e-21119
CD14-positive, CD16-negative classical monocyte3.22e-2042
hematopoietic lineage restricted progenitor cell1.70e-18124
classical monocyte1.42e-1745
myeloid leukocyte1.38e-1676
monopoietic cell5.16e-1463
monocyte5.16e-1463
monoblast5.16e-1463
promonocyte5.16e-1463
macrophage dendritic cell progenitor4.19e-1365
granulocyte monocyte progenitor cell4.93e-1371
hematopoietic stem cell2.06e-12172
angioblastic mesenchymal cell2.06e-12172
myeloid lineage restricted progenitor cell2.85e-1270
hematopoietic oligopotent progenitor cell3.62e-11165
hematopoietic multipotent progenitor cell3.62e-11165
hematopoietic cell6.01e-10182
lymphoid lineage restricted progenitor cell1.48e-0752
lymphocyte3.54e-0753
common lymphoid progenitor3.54e-0753
Uber Anatomy
Ontology termp-valuen
adult organism4.66e-16115
hematopoietic system8.02e-15102
blood island8.02e-15102
hemolymphoid system1.94e-14112
bone marrow1.87e-1280
bone element6.31e-1086
immune system4.87e-09115
skeletal element6.58e-09101
skeletal system6.58e-09101
neural tube7.40e-0757
neural rod7.40e-0757
future spinal cord7.40e-0757
neural keel7.40e-0757
regional part of brain8.63e-0759


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
STAT1#6772315.52994062289940.000434088655175550.00405036943249167
STAT2#6773348.94782838983051.42094046481278e-050.00034029259620404
SUZ12#23512225.05789045553150.002325256716520610.0131860501828037
ZBTB33#10009215.83236251499060.005734248930324640.0258404911992654



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.