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Coexpression cluster:C4009: Difference between revisions

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|ontology_enrichment_disease=DOID:14566!1.35e-09!239;DOID:162!2.78e-09!235;DOID:2531!1.60e-07!51;DOID:0060083!1.60e-07!51;DOID:0050686!1.77e-07!137
|ontology_enrichment_disease=DOID:14566!1.35e-09!239;DOID:162!2.78e-09!235;DOID:2531!1.60e-07!51;DOID:0060083!1.60e-07!51;DOID:0050686!1.77e-07!137
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tf_chipseq_enrich=KAT2A#2648;1:205.363333333333:0.00486154522073778:0.0227540970381211!ZZZ3#26009;1:79.8044041450777:0.012478437908258:0.0451649827309151
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}}
}}

Revision as of 11:43, 5 September 2012


Full id: C4009_CD4_CD133_CD8_CD19_choriocarcinoma_Retinal_CD34



Phase1 CAGE Peaks

Hg19::chr1:93297586..93297609,+p1@RPL5
Hg19::chr5:130325570..130325577,+p1@ENST00000498453
Hg19::chr7:156985019..156985030,+p1@ENST00000429552


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:00080975S rRNA binding0.00353232073472271
GO:0019843rRNA binding0.0153067231837984
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)0.0153067231837984
GO:0005830cytosolic ribosome (sensu Eukaryota)0.0220770045920169
GO:0015934large ribosomal subunit0.024726245143059
GO:0044445cytosolic part0.0372856077554064
GO:0033279ribosomal subunit0.0376780878370422



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><br>disease_data<br>


Cell Type
Ontology termp-valuen
lymphocyte8.87e-2453
common lymphoid progenitor8.87e-2453
lymphoid lineage restricted progenitor cell2.95e-2352
nongranular leukocyte4.60e-23119
hematopoietic stem cell2.15e-21172
angioblastic mesenchymal cell2.15e-21172
hematopoietic lineage restricted progenitor cell4.28e-21124
hematopoietic oligopotent progenitor cell1.21e-19165
hematopoietic multipotent progenitor cell1.21e-19165
leukocyte5.21e-19140
hematopoietic cell2.57e-18182
lymphocyte of B lineage2.92e-1224
pro-B cell2.92e-1224
T cell2.54e-1125
pro-T cell2.54e-1125
mature alpha-beta T cell5.62e-1118
alpha-beta T cell5.62e-1118
immature T cell5.62e-1118
mature T cell5.62e-1118
immature alpha-beta T cell5.62e-1118
native cell1.14e-09722
B cell4.70e-0914
classical monocyte2.32e-0845
CD14-positive, CD16-negative classical monocyte4.24e-0842
CD8-positive, alpha-beta T cell6.34e-0811
Disease
Ontology termp-valuen
disease of cellular proliferation1.35e-09239
cancer2.78e-09235
hematologic cancer1.60e-0751
immune system cancer1.60e-0751
organ system cancer1.77e-07137


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
KAT2A#26481205.3633333333330.004861545220737780.0227540970381211
ZZZ3#26009179.80440414507770.0124784379082580.0451649827309151



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.