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Coexpression cluster:C1609: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!6.37e-16!102;UBERON:0003061!6.37e-16!102;UBERON:0002193!6.89e-14!112;UBERON:0002371!9.49e-14!80;UBERON:0001474!2.06e-13!86;UBERON:0004765!5.33e-10!101;UBERON:0001434!5.33e-10!101;UBERON:0002405!8.79e-10!115
|ontology_enrichment_uberon=UBERON:0002390!6.37e-16!102;UBERON:0003061!6.37e-16!102;UBERON:0002193!6.89e-14!112;UBERON:0002371!9.49e-14!80;UBERON:0001474!2.06e-13!86;UBERON:0004765!5.33e-10!101;UBERON:0001434!5.33e-10!101;UBERON:0002405!8.79e-10!115
|tf_chipseq_enrich=ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447226506384368!FOS#2353;3:5.39877318533664:0.0115389531727874:0.0421841476621656!GATA2#2624;3:7.6469590401324:0.00427906187925213:0.0203275389405146!JUN#3725;3:7.5076975154018:0.00451120655290603:0.0213323327528277!MAX#4149;4:5.1620444072057:0.00252630900948518:0.0139956071844697
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}}
}}

Revision as of 14:34, 5 September 2012


Full id: C1609_CD4_CD34_Mast_CD14_CD19_CD133_Peripheral



Phase1 CAGE Peaks

Hg19::chr11:116864496..116864504,+p@chr11:116864496..116864504
+
Hg19::chr2:238512335..238512368,-p@chr2:238512335..238512368
-
Hg19::chr2:238512370..238512394,-p@chr2:238512370..238512394
-
Hg19::chr2:238512518..238512533,+p@chr2:238512518..238512533
+
Hg19::chr5:43042577..43042600,+p2@LOC153684


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><br>


Cell Type
Ontology termp-valuen
leukocyte2.44e-33140
hematopoietic stem cell3.08e-33172
angioblastic mesenchymal cell3.08e-33172
nongranular leukocyte4.57e-33119
hematopoietic oligopotent progenitor cell2.92e-31165
hematopoietic multipotent progenitor cell2.92e-31165
hematopoietic lineage restricted progenitor cell1.50e-30124
hematopoietic cell9.25e-29182
CD14-positive, CD16-negative classical monocyte7.33e-2842
classical monocyte1.92e-2545
myeloid leukocyte7.72e-1876
granulocyte monocyte progenitor cell5.62e-1771
myeloid cell6.20e-16112
common myeloid progenitor6.20e-16112
monopoietic cell7.71e-1663
monocyte7.71e-1663
monoblast7.71e-1663
promonocyte7.71e-1663
myeloid lineage restricted progenitor cell1.01e-1570
macrophage dendritic cell progenitor1.85e-1565
lymphocyte3.43e-1553
common lymphoid progenitor3.43e-1553
lymphoid lineage restricted progenitor cell4.44e-1552
mature alpha-beta T cell3.09e-1218
alpha-beta T cell3.09e-1218
immature T cell3.09e-1218
mature T cell3.09e-1218
immature alpha-beta T cell3.09e-1218
T cell2.57e-0925
pro-T cell2.57e-0925
B cell1.43e-0814
CD8-positive, alpha-beta T cell1.51e-0711
intermediate monocyte7.20e-079
CD14-positive, CD16-positive monocyte7.20e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.37e-16102
blood island6.37e-16102
hemolymphoid system6.89e-14112
bone marrow9.49e-1480
bone element2.06e-1386
skeletal element5.33e-10101
skeletal system5.33e-10101
immune system8.79e-10115


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
ELF1#199743.406478367046030.01235066105299550.0447226506384368
FOS#235335.398773185336640.01153895317278740.0421841476621656
GATA2#262437.64695904013240.004279061879252130.0203275389405146
JUN#372537.50769751540180.004511206552906030.0213323327528277
MAX#414945.16204440720570.002526309009485180.0139956071844697



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.