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Coexpression cluster:C1627: Difference between revisions

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|tf_chipseq_enrich=EBF1#1879;3:5.3438801079414:0.0118761556386811:0.0432277495817175!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.0057252811633537!TAL1#6886;2:11.9474466709761:0.010475778180992:0.0387999077042564
|tf_chipseq_enrich=EBF1#1879;3:5.3438801079414:0.0118761556386811:0.0432277495817175!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.0057252811633537!TAL1#6886;2:11.9474466709761:0.010475778180992:0.0387999077042564
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}}
}}

Revision as of 15:00, 26 November 2012


Full id: C1627_Whole_Neutrophils_CD14CD16_CD14_blood_CD8_Eosinophils



Phase1 CAGE Peaks

Hg19::chr11:2323089..2323154,-p1@C11orf21
Hg19::chr11:2323349..2323407,+p1@TSPAN32
Hg19::chr12:51717875..51717920,-p1@BIN2
Hg19::chr21:46340976..46341000,+p1@ENST00000441379
p1@uc002zgh.2
Hg19::chr9:21031615..21031651,-p1@PTPLAD2


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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell2.62e-90168
angioblastic mesenchymal cell2.62e-90168
hematopoietic oligopotent progenitor cell6.89e-85161
hematopoietic multipotent progenitor cell6.89e-85161
hematopoietic cell1.28e-82177
leukocyte2.16e-75136
hematopoietic lineage restricted progenitor cell1.35e-63120
nongranular leukocyte6.97e-61115
myeloid cell3.62e-56108
common myeloid progenitor3.62e-56108
myeloid leukocyte2.40e-4372
granulocyte monocyte progenitor cell3.71e-3867
myeloid lineage restricted progenitor cell3.33e-3766
macrophage dendritic cell progenitor1.05e-3361
monopoietic cell5.91e-3359
monocyte5.91e-3359
monoblast5.91e-3359
promonocyte5.91e-3359
defensive cell5.81e-3048
phagocyte5.81e-3048
classical monocyte5.13e-2942
CD14-positive, CD16-negative classical monocyte5.13e-2942
nucleate cell2.10e-2455
lymphocyte1.14e-2353
common lymphoid progenitor1.14e-2353
lymphoid lineage restricted progenitor cell1.82e-2352
connective tissue cell7.61e-19361
mesenchymal cell1.79e-18354
mature alpha-beta T cell3.82e-1518
alpha-beta T cell3.82e-1518
immature T cell3.82e-1518
mature T cell3.82e-1518
immature alpha-beta T cell3.82e-1518
T cell3.79e-1325
pro-T cell3.79e-1325
motile cell9.81e-13386
CD8-positive, alpha-beta T cell3.46e-1111
intermediate monocyte2.28e-099
CD14-positive, CD16-positive monocyte2.28e-099
lymphocyte of B lineage4.03e-0924
pro-B cell4.03e-0924
stuff accumulating cell8.14e-0987
multi fate stem cell1.37e-08427
stem cell2.76e-08441
granulocyte3.89e-088
somatic stem cell6.32e-08433
B cell2.12e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.25e-4498
blood island8.25e-4498
hemolymphoid system6.37e-39108
bone marrow1.81e-3376
immune system4.82e-3193
bone element4.22e-2982
skeletal element1.47e-2790
skeletal system1.23e-23100
connective tissue2.02e-17371
lateral plate mesoderm5.95e-12203
blood1.23e-0815
haemolymphatic fluid1.23e-0815
organism substance1.23e-0815
adult organism2.32e-08114
musculoskeletal system2.58e-07167
Disease
Ontology termp-valuen
myeloid leukemia2.97e-1131
leukemia4.80e-1139
hematologic cancer5.26e-1051
immune system cancer5.26e-1051


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
EBF1#187935.34388010794140.01187615563868110.0432277495817175
ELF1#199754.258097958807540.0007142416939776840.0057252811633537
TAL1#6886211.94744667097610.0104757781809920.0387999077042564



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.