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Coexpression cluster:C2215: Difference between revisions

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|tf_chipseq_enrich=NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00766855109619694!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227541808511589!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321429969381632!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243602590654099
|tf_chipseq_enrich=NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00766855109619694!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227541808511589!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321429969381632!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243602590654099
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}}
}}

Revision as of 15:22, 26 November 2012


Full id: C2215_CD14CD16_CD4_CD8_CD19_CD14_Basophils_Whole



Phase1 CAGE Peaks

Hg19::chr12:53689319..53689349,+p1@PFDN5
Hg19::chr1:160681597..160681619,-p1@CD48
Hg19::chr6:29691170..29691188,+p2@HLA-F
Hg19::chr6:32811861..32811872,+p1@LOC100507463


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
leukocyte4.01e-58136
nongranular leukocyte1.98e-49115
hematopoietic lineage restricted progenitor cell4.34e-49120
hematopoietic stem cell7.95e-46168
angioblastic mesenchymal cell7.95e-46168
hematopoietic oligopotent progenitor cell1.20e-42161
hematopoietic multipotent progenitor cell1.20e-42161
hematopoietic cell1.86e-41177
myeloid leukocyte5.09e-2972
defensive cell3.23e-2648
phagocyte3.23e-2648
granulocyte monocyte progenitor cell3.13e-2567
macrophage dendritic cell progenitor5.70e-2561
myeloid lineage restricted progenitor cell7.00e-2566
monopoietic cell2.64e-2459
monocyte2.64e-2459
monoblast2.64e-2459
promonocyte2.64e-2459
classical monocyte6.19e-2442
CD14-positive, CD16-negative classical monocyte6.19e-2442
nucleate cell1.80e-2255
lymphocyte1.84e-2253
common lymphoid progenitor1.84e-2253
lymphoid lineage restricted progenitor cell3.61e-2252
myeloid cell6.35e-20108
common myeloid progenitor6.35e-20108
mesenchymal cell5.35e-13354
connective tissue cell1.69e-12361
lymphocyte of B lineage1.02e-1124
pro-B cell1.02e-1124
mature alpha-beta T cell9.06e-1118
alpha-beta T cell9.06e-1118
immature T cell9.06e-1118
mature T cell9.06e-1118
immature alpha-beta T cell9.06e-1118
T cell1.74e-1025
pro-T cell1.74e-1025
stuff accumulating cell1.21e-0987
B cell9.08e-0914
multi fate stem cell7.84e-08427
CD8-positive, alpha-beta T cell1.30e-0711
motile cell1.54e-07386
somatic stem cell7.11e-07433
stem cell8.16e-07441
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.31e-3298
blood island6.31e-3298
hemolymphoid system1.37e-29108
immune system1.68e-2393
bone marrow4.42e-2376
bone element6.78e-1882
skeletal element1.35e-1690
skeletal system1.80e-14100
connective tissue1.42e-11371
lateral plate mesoderm3.33e-10203
adult organism1.22e-07114
blood4.25e-0715
haemolymphatic fluid4.25e-0715
organism substance4.25e-0715


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
NFKB1#479045.488063424193840.001102199566301980.00766855109619694
POU2F2#545236.829593043306890.004860473775203740.0227541808511589
TAF1#687243.343046285745290.008005664898701650.0321429969381632
TBP#690843.706770687096390.005296377814784350.0243602590654099



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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