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Coexpression cluster:C4692: Difference between revisions

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|ontology_enrichment_disease=DOID:1240!7.98e-15!39;DOID:8692!1.83e-13!31;DOID:2531!3.90e-13!51;DOID:0060083!3.90e-13!51
|ontology_enrichment_disease=DOID:1240!7.98e-15!39;DOID:8692!1.83e-13!31;DOID:2531!3.90e-13!51;DOID:0060083!3.90e-13!51
|ontology_enrichment_uberon=UBERON:0002371!5.73e-35!80;UBERON:0002193!7.66e-33!112;UBERON:0001474!1.89e-32!86;UBERON:0002390!1.23e-31!102;UBERON:0003061!1.23e-31!102;UBERON:0002405!2.19e-27!115;UBERON:0004765!1.94e-26!101;UBERON:0001434!1.94e-26!101;UBERON:0003081!5.58e-14!216;UBERON:0002204!1.83e-13!167;UBERON:0002384!5.85e-11!375
|ontology_enrichment_uberon=UBERON:0002371!5.73e-35!80;UBERON:0002193!7.66e-33!112;UBERON:0001474!1.89e-32!86;UBERON:0002390!1.23e-31!102;UBERON:0003061!1.23e-31!102;UBERON:0002405!2.19e-27!115;UBERON:0004765!1.94e-26!101;UBERON:0001434!1.94e-26!101;UBERON:0003081!5.58e-14!216;UBERON:0002204!1.83e-13!167;UBERON:0002384!5.85e-11!375
|tf_chipseq_enrich=GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154808957593432!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393572060283661!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376476388901085
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}}
}}

Revision as of 14:15, 5 September 2012


Full id: C4692_anaplastic_cord_Dendritic_hairy_chronic_CD14_acute



Phase1 CAGE Peaks

Hg19::chr7:643123..643163,+p@chr7:643123..643163
+
Hg19::chr7:643166..643188,+p@chr7:643166..643188
+
Hg19::chr7:643196..643205,+p@chr7:643196..643205
+


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

No GOStat results

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>disease_data<br>

Cell Type
Ontology termp-valuen
myeloid cell1.21e-47112
common myeloid progenitor1.21e-47112
hematopoietic cell1.60e-44182
granulocyte monocyte progenitor cell2.14e-4071
hematopoietic oligopotent progenitor cell4.73e-40165
hematopoietic multipotent progenitor cell4.73e-40165
myeloid lineage restricted progenitor cell1.37e-3970
hematopoietic stem cell3.12e-39172
angioblastic mesenchymal cell3.12e-39172
monopoietic cell3.13e-3963
monocyte3.13e-3963
monoblast3.13e-3963
promonocyte3.13e-3963
macrophage dendritic cell progenitor4.03e-3965
myeloid leukocyte7.66e-3876
CD14-positive, CD16-negative classical monocyte2.92e-3542
classical monocyte6.98e-3245
hematopoietic lineage restricted progenitor cell3.63e-29124
leukocyte1.51e-28140
nongranular leukocyte7.05e-28119
connective tissue cell3.16e-11365
mesenchymal cell3.73e-11358
motile cell4.61e-09390
multi fate stem cell1.78e-08430
somatic stem cell5.98e-08436
stem cell6.43e-08444
Uber Anatomy
Ontology termp-valuen
bone marrow5.73e-3580
hemolymphoid system7.66e-33112
bone element1.89e-3286
hematopoietic system1.23e-31102
blood island1.23e-31102
immune system2.19e-27115
skeletal element1.94e-26101
skeletal system1.94e-26101
lateral plate mesoderm5.58e-14216
musculoskeletal system1.83e-13167
connective tissue5.85e-11375
Disease
Ontology termp-valuen
leukemia7.98e-1539
myeloid leukemia1.83e-1331
hematologic cancer3.90e-1351
immune system cancer3.90e-1351


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
GABPB1#255337.067683836182170.002832212825417420.0154808957593432
HDAC2#3066313.41562023662630.0004140761399857210.00393572060283661
SRF#6722313.79717826216780.0003806615025800190.00376476388901085



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.

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