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Coexpression cluster:C4229: Difference between revisions

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|tf_chipseq_enrich=FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0225970520001594!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246836509233368!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460581525572201!PPARGC1A#10891;1:116.683712121212:0.00854576321178668:0.0325698268100496
|tf_chipseq_enrich=FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0225970520001594!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246836509233368!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460581525572201!PPARGC1A#10891;1:116.683712121212:0.00854576321178668:0.0325698268100496
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}}
}}

Revision as of 16:37, 26 November 2012


Full id: C4229_Eosinophils_mature_skeletal_Neutrophils_Hepatocyte_pituitary_Whole



Phase1 CAGE Peaks

Hg19::chr2:43454125..43454146,-p2@ZFP36L2
Hg19::chr4:185734844..185734848,+p1@ENST00000508020
Hg19::chr7:106061649..106061650,+p@chr7:106061649..106061650
+


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:0000288mRNA catabolic process, deadenylation-dependent decay0.00345382471839554
GO:0043487regulation of RNA stability0.00345382471839554
GO:0043488regulation of mRNA stability0.00345382471839554
GO:0051252regulation of RNA metabolic process0.00615212527964205
GO:0006402mRNA catabolic process0.00751206876251031
GO:0006401RNA catabolic process0.00992974606538718



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
myeloid leukocyte8.61e-3172
classical monocyte2.25e-3042
CD14-positive, CD16-negative classical monocyte2.25e-3042
defensive cell1.56e-2548
phagocyte1.56e-2548
monopoietic cell2.26e-2059
monocyte2.26e-2059
monoblast2.26e-2059
promonocyte2.26e-2059
stuff accumulating cell1.54e-1987
macrophage dendritic cell progenitor1.90e-1961
myeloid lineage restricted progenitor cell7.70e-1966
granulocyte monocyte progenitor cell1.94e-1867
granulocyte6.21e-188
myeloid cell5.53e-17108
common myeloid progenitor5.53e-17108
leukocyte3.59e-16136
blood cell1.50e-1211
hematopoietic stem cell9.68e-12168
angioblastic mesenchymal cell9.68e-12168
nongranular leukocyte7.24e-11115
hematopoietic cell1.39e-10177
hematopoietic oligopotent progenitor cell1.62e-09161
hematopoietic multipotent progenitor cell1.62e-09161
intermediate monocyte2.25e-089
CD14-positive, CD16-positive monocyte2.25e-089
hematopoietic lineage restricted progenitor cell2.36e-08120
neutrophil4.43e-083
single nucleate cell2.30e-073
mononuclear cell2.30e-073
basophil3.59e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.71e-2098
blood island2.71e-2098
hemolymphoid system1.60e-18108
bone marrow1.32e-1676
immune system3.03e-1693
bone element8.61e-1582
skeletal element9.24e-1390
skeletal system1.06e-10100
adult organism7.53e-10114
lateral plate mesoderm5.37e-08203


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)

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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
FOXA2#3170216.42030916844350.004810682352105480.0225970520001594
HNF4A#3172215.42152690863580.005444210486686610.0246836509233368
NR3C1#290829.982015554115360.01278474365547170.0460581525572201
PPARGC1A#108911116.6837121212120.008545763211786680.0325698268100496



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.