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Coexpression cluster:C3712: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3712_granulocyte_Neutrophils_embryonic_non_Eosinophils_CD19_rectum
|full_id=C3712_granulocyte_Neutrophils_embryonic_non_Eosinophils_CD19_rectum
|gostat_on_coexpression_clusters=GO:0005158!insulin receptor binding!0.0263626274788933!55023$GO:0008286!insulin receptor signaling pathway!0.0263626274788933!55023
|gostat_on_coexpression_clusters=GO:0005158!insulin receptor binding!0.0263626274788933!55023$GO:0008286!insulin receptor signaling pathway!0.0263626274788933!55023

Revision as of 16:40, 12 September 2012


Full id: C3712_granulocyte_Neutrophils_embryonic_non_Eosinophils_CD19_rectum



Phase1 CAGE Peaks

Hg19::chr18:2655849..2655941,+p2@SMCHD1
Hg19::chr6:79787902..79787958,-p1@PHIP
Hg19::chr6:79787964..79787994,-p2@PHIP


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


GO IDGO nameFDR corrected p-value
GO:0005158insulin receptor binding0.0263626274788933
GO:0008286insulin receptor signaling pathway0.0263626274788933



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
hematopoietic stem cell1.97e-39172
angioblastic mesenchymal cell1.97e-39172
leukocyte5.39e-36140
hematopoietic oligopotent progenitor cell6.35e-36165
hematopoietic multipotent progenitor cell6.35e-36165
hematopoietic cell2.06e-34182
hematopoietic lineage restricted progenitor cell3.37e-29124
nongranular leukocyte2.81e-28119
myeloid cell1.40e-18112
common myeloid progenitor1.40e-18112
lymphocyte8.84e-1753
common lymphoid progenitor8.84e-1753
lymphoid lineage restricted progenitor cell1.53e-1652
myeloid leukocyte2.13e-1576
granulocyte monocyte progenitor cell3.04e-1371
myeloid lineage restricted progenitor cell1.56e-1270
classical monocyte6.28e-1245
CD14-positive, CD16-negative classical monocyte1.16e-1142
macrophage dendritic cell progenitor4.00e-1165
monopoietic cell1.29e-1063
monocyte1.29e-1063
monoblast1.29e-1063
promonocyte1.29e-1063
T cell1.83e-0925
pro-T cell1.83e-0925
mature alpha-beta T cell2.57e-0918
alpha-beta T cell2.57e-0918
immature T cell2.57e-0918
mature T cell2.57e-0918
immature alpha-beta T cell2.57e-0918
B cell2.01e-0714
lymphocyte of B lineage5.52e-0724
pro-B cell5.52e-0724
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.73e-16102
blood island7.73e-16102
adult organism1.02e-15115
hemolymphoid system4.04e-13112
bone element1.10e-0986
bone marrow1.17e-0980
central nervous system8.79e-0982
neural tube1.31e-0857
neural rod1.31e-0857
future spinal cord1.31e-0857
neural keel1.31e-0857
regional part of nervous system3.09e-0894
nervous system3.09e-0894
anterior neural tube1.87e-0742
brain3.44e-0769
future brain3.44e-0769
regional part of forebrain4.27e-0741
forebrain4.27e-0741
future forebrain4.27e-0741
regional part of brain5.47e-0759
skeletal element7.80e-07101
skeletal system7.80e-07101


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
CCNT2#90536.336201576962630.003930750035764890.01898989744589
EGR1#195834.988179094810140.008056488137383440.0320452284945039
ELF1#199734.258097958807540.01295179875054610.046193112376064
GATA1#2623313.56030814380040.0004009615963782630.00387741001519902
HDAC2#3066313.41562023662630.0004140761399857210.00391151392763827
NFKB1#479035.488063424193840.006049381815655430.026944361457064
NFYB#4801211.17319550235760.01025467135054530.0381242923672077
PBX3#5090214.60967512449610.006056122473217890.0268279341270955
POU2F2#545239.106124057742520.001324165192682130.00881755219067387
RXRA#6256213.38307809275550.007196434429465730.0298273043645913
SIN3A#2594235.408884726815140.006318961977991520.0276498269657892
TFAP2C#7022310.80922860986020.0007916746575753130.00615649363831036
TRIM28#10155212.39368336350830.008368344129438470.0329059296887961
YY1#752834.911170749853860.008441455341808260.0329121273170983



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.