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Coexpression cluster:C4369: Difference between revisions

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|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464070574210335!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277708327730793!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0330057762133073
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464070574210335!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277708327730793!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0330057762133073
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}}
}}

Revision as of 16:42, 26 November 2012


Full id: C4369_Eosinophils_CD14_Natural_Neutrophils_CD19_CD8_CD4



Phase1 CAGE Peaks

Hg19::chr4:130017338..130017347,+p4@C4orf33
Hg19::chr6:30181374..30181395,+p@chr6:30181374..30181395
+
Hg19::chr6:30181883..30181935,-p@chr6:30181883..30181935
-


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
leukocyte5.72e-70136
nongranular leukocyte2.22e-57115
hematopoietic lineage restricted progenitor cell6.95e-54120
hematopoietic stem cell4.05e-52168
angioblastic mesenchymal cell4.05e-52168
hematopoietic cell2.63e-50177
hematopoietic oligopotent progenitor cell3.02e-48161
hematopoietic multipotent progenitor cell3.02e-48161
classical monocyte5.62e-3942
CD14-positive, CD16-negative classical monocyte5.62e-3942
myeloid leukocyte1.77e-3672
defensive cell2.51e-3248
phagocyte2.51e-3248
lymphocyte3.26e-2853
common lymphoid progenitor3.26e-2853
lymphoid lineage restricted progenitor cell1.83e-2752
nucleate cell1.09e-2655
myeloid lineage restricted progenitor cell2.69e-2666
granulocyte monocyte progenitor cell1.09e-2567
monopoietic cell1.21e-2459
monocyte1.21e-2459
monoblast1.21e-2459
promonocyte1.21e-2459
macrophage dendritic cell progenitor2.08e-2361
myeloid cell1.55e-20108
common myeloid progenitor1.55e-20108
lymphocyte of B lineage3.95e-1724
pro-B cell3.95e-1724
mesenchymal cell2.63e-12354
stuff accumulating cell4.30e-1287
connective tissue cell5.39e-12361
intermediate monocyte6.16e-129
CD14-positive, CD16-positive monocyte6.16e-129
granulocyte1.11e-118
B cell3.11e-1114
blood cell9.42e-1011
motile cell1.02e-09386
mature alpha-beta T cell4.59e-0918
alpha-beta T cell4.59e-0918
immature T cell4.59e-0918
mature T cell4.59e-0918
immature alpha-beta T cell4.59e-0918
T cell6.77e-0925
pro-T cell6.77e-0925
CD4-positive, alpha-beta T cell1.24e-086
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.44e-3398
blood island4.44e-3398
hemolymphoid system3.48e-29108
bone marrow7.51e-2576
immune system1.35e-2493
bone element5.86e-2382
skeletal element1.52e-2090
skeletal system5.51e-17100
connective tissue2.10e-11371
lateral plate mesoderm8.43e-09203


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#199734.258097958807540.01295179875054610.0464070574210335
SIN3A#2594235.408884726815140.006318961977991520.0277708327730793
SMARCB1#6598212.16847718743830.008675002221921740.0330057762133073



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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