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Coexpression cluster:C4501: Difference between revisions

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|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464452997427648!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0330105864991359
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464452997427648!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0330105864991359
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}}
}}

Revision as of 16:46, 26 November 2012


Full id: C4501_Natural_CD14_CD4_CD8_Peripheral_CD34_Basophils



Phase1 CAGE Peaks

Hg19::chr5:42950094..42950117,+p@chr5:42950094..42950117
+
Hg19::chr5:42994673..42994693,-p@chr5:42994673..42994693
-
Hg19::chr8:29387130..29387137,+p@chr8:29387130..29387137
+


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
leukocyte4.79e-68136
hematopoietic lineage restricted progenitor cell8.95e-67120
hematopoietic stem cell1.62e-61168
angioblastic mesenchymal cell1.62e-61168
hematopoietic cell1.60e-60177
nongranular leukocyte9.45e-60115
hematopoietic oligopotent progenitor cell5.03e-59161
hematopoietic multipotent progenitor cell5.03e-59161
myeloid lineage restricted progenitor cell3.06e-4466
granulocyte monocyte progenitor cell1.72e-4367
myeloid leukocyte2.05e-4372
classical monocyte2.61e-4142
CD14-positive, CD16-negative classical monocyte2.61e-4142
macrophage dendritic cell progenitor4.46e-3961
myeloid cell3.46e-37108
common myeloid progenitor3.46e-37108
monopoietic cell5.47e-3759
monocyte5.47e-3759
monoblast5.47e-3759
promonocyte5.47e-3759
defensive cell5.45e-3648
phagocyte5.45e-3648
mesenchymal cell2.92e-21354
nucleate cell2.24e-2055
connective tissue cell3.49e-20361
lymphoid lineage restricted progenitor cell2.42e-1952
lymphocyte9.19e-1953
common lymphoid progenitor9.19e-1953
motile cell6.09e-17386
stuff accumulating cell2.58e-1687
T cell3.31e-1525
pro-T cell3.31e-1525
mature alpha-beta T cell5.98e-1518
alpha-beta T cell5.98e-1518
immature T cell5.98e-1518
mature T cell5.98e-1518
immature alpha-beta T cell5.98e-1518
multi fate stem cell2.31e-13427
stem cell5.68e-13441
somatic stem cell9.98e-13433
intermediate monocyte2.78e-109
CD14-positive, CD16-positive monocyte2.78e-109
CD4-positive, alpha-beta T cell4.93e-096
CD8-positive, alpha-beta T cell2.71e-0711
circulating cell5.42e-076
histamine secreting cell6.88e-075
biogenic amine secreting cell6.88e-075
granulocytopoietic cell6.88e-075
mast cell6.88e-075
mast cell progenitor6.88e-075
basophil mast progenitor cell6.88e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.17e-4398
blood island8.17e-4398
hemolymphoid system3.66e-39108
bone marrow7.90e-3876
immune system7.96e-3893
bone element3.39e-3682
skeletal element2.96e-3190
skeletal system3.14e-26100
connective tissue6.17e-20371
lateral plate mesoderm1.16e-12203
musculoskeletal system6.03e-10167


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#199734.258097958807540.01295179875054610.0464452997427648
SMARCB1#6598212.16847718743830.008675002221921740.0330105864991359



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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