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Coexpression cluster:C4106: Difference between revisions

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|tf_chipseq_enrich=FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582223871310268!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128344172689684!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247006197472151
|tf_chipseq_enrich=FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582223871310268!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128344172689684!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247006197472151
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}}
}}

Revision as of 16:33, 26 November 2012


Full id: C4106_Monocytederived_Melanocyte_Macrophage_granulocyte_Dendritic_acute_CD14



Phase1 CAGE Peaks

Hg19::chr22:45636692..45636714,-p4@KIAA0930
Hg19::chr22:45636717..45636734,-p5@KIAA0930
Hg19::chr22:45636741..45636810,-p1@KIAA0930


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
monopoietic cell1.64e-2659
monocyte1.64e-2659
monoblast1.64e-2659
promonocyte1.64e-2659
macrophage dendritic cell progenitor4.23e-2661
myeloid lineage restricted progenitor cell5.03e-2566
granulocyte monocyte progenitor cell7.12e-2567
myeloid leukocyte4.21e-2472
defensive cell1.68e-2148
phagocyte1.68e-2148
myeloid cell4.80e-19108
common myeloid progenitor4.80e-19108
classical monocyte1.51e-1742
CD14-positive, CD16-negative classical monocyte1.51e-1742
stuff accumulating cell4.64e-1587
nongranular leukocyte2.09e-11115
hematopoietic stem cell5.49e-11168
angioblastic mesenchymal cell5.49e-11168
leukocyte5.89e-11136
hematopoietic cell8.17e-11177
hematopoietic lineage restricted progenitor cell9.79e-11120
hematopoietic oligopotent progenitor cell5.79e-10161
hematopoietic multipotent progenitor cell5.79e-10161
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.27e-1998
blood island1.27e-1998
bone marrow5.03e-1976
hemolymphoid system3.86e-18108
bone element1.14e-1682
immune system2.59e-1693
skeletal element2.19e-1590
skeletal system2.30e-12100
adult organism7.06e-09114
telencephalon2.89e-0834
brain grey matter6.42e-0834
gray matter6.42e-0834
neural tube1.12e-0756
neural rod1.12e-0756
future spinal cord1.12e-0756
neural keel1.12e-0756
regional part of telencephalon1.61e-0732
cerebral hemisphere2.06e-0732
organ2.10e-07503
regional part of cerebral cortex3.26e-0722
regional part of nervous system6.69e-0753
regional part of brain6.69e-0753
developing anatomical structure7.94e-07581
anatomical group9.72e-07625


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
FOXA1#3169311.08141974938550.000734755275698670.00582223871310268
IRF1#365937.63716375356390.002244692747297240.0128344172689684
SP1#666735.69838137814090.005403962701712170.0247006197472151



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.