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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C622_CD19_CD14_immature_Peripheral_Neutrophils_Natural_CD8
|full_id=C622_CD19_CD14_immature_Peripheral_Neutrophils_Natural_CD8
|gostat_on_coexpression_clusters=GO:0051085!chaperone cofactor-dependent protein folding!0.0334245397562372!64222$GO:0006458!'de novo' protein folding!0.0334245397562372!64222$GO:0051084!'de novo' posttranslational protein folding!0.0334245397562372!64222$GO:0005669!transcription factor TFIID complex!0.0469838878480247!6881
|gostat_on_coexpression_clusters=GO:0051085!chaperone cofactor-dependent protein folding!0.0334245397562372!64222$GO:0006458!'de novo' protein folding!0.0334245397562372!64222$GO:0051084!'de novo' posttranslational protein folding!0.0334245397562372!64222$GO:0005669!transcription factor TFIID complex!0.0469838878480247!6881

Revision as of 18:16, 12 September 2012


Full id: C622_CD19_CD14_immature_Peripheral_Neutrophils_Natural_CD8



Phase1 CAGE Peaks

Hg19::chr11:6633799..6633813,-p11@TAF10
Hg19::chr16:19222406..19222410,-p@chr16:19222406..19222410
-
Hg19::chr1:1005339..1005350,-p@chr1:1005339..1005350
-
Hg19::chr1:179050670..179050709,+p3@TOR3A
Hg19::chr1:226298353..226298372,-p@chr1:226298353..226298372
-
Hg19::chr2:33701603..33701615,-p@chr2:33701603..33701615
-
Hg19::chr2:88905814..88905819,-p@chr2:88905814..88905819
-
Hg19::chr2:88909458..88909464,-p1@AK129635
Hg19::chr4:103680719..103680723,-p@chr4:103680719..103680723
-
Hg19::chr5:149790235..149790248,-p@chr5:149790235..149790248
-
Hg19::chr6:14127098..14127123,+p@chr6:14127098..14127123
+
Hg19::chr6:14127175..14127200,+p@chr6:14127175..14127200
+
Hg19::chr6:167507740..167507764,+p@chr6:167507740..167507764
+
Hg19::chr8:102218459..102218472,-p8@ZNF706


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:0051085chaperone cofactor-dependent protein folding0.0334245397562372
GO:0006458'de novo' protein folding0.0334245397562372
GO:0051084'de novo' posttranslational protein folding0.0334245397562372
GO:0005669transcription factor TFIID complex0.0469838878480247



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
leukocyte2.21e-59140
hematopoietic stem cell1.35e-52172
angioblastic mesenchymal cell1.35e-52172
hematopoietic cell4.84e-50182
hematopoietic oligopotent progenitor cell1.36e-48165
hematopoietic multipotent progenitor cell1.36e-48165
nongranular leukocyte6.70e-48119
hematopoietic lineage restricted progenitor cell2.44e-46124
myeloid leukocyte9.71e-3176
granulocyte monocyte progenitor cell4.90e-2871
myeloid cell1.24e-26112
common myeloid progenitor1.24e-26112
macrophage dendritic cell progenitor6.16e-2665
monopoietic cell1.12e-2463
monocyte1.12e-2463
monoblast1.12e-2463
promonocyte1.12e-2463
CD14-positive, CD16-negative classical monocyte1.88e-2442
myeloid lineage restricted progenitor cell3.51e-2470
classical monocyte5.34e-2245
lymphocyte4.66e-2053
common lymphoid progenitor4.66e-2053
lymphoid lineage restricted progenitor cell1.26e-1952
lymphocyte of B lineage2.87e-1324
pro-B cell2.87e-1324
B cell4.30e-0914
mesenchymal cell2.97e-08358
connective tissue cell2.56e-07365
dendritic cell3.29e-0710
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.24e-33102
blood island2.24e-33102
hemolymphoid system1.10e-29112
bone marrow6.89e-2580
bone element1.38e-2386
immune system3.53e-19115
skeletal element8.82e-17101
skeletal system8.82e-17101
connective tissue1.47e-07375
blood2.99e-0715
haemolymphatic fluid2.99e-0715
organism substance2.99e-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#479072.744031712096920.006869951901034420.0290965126968707
POU2F2#545253.252187163479470.01362351556019460.0480733297831254



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.