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|gostat_on_coexpression_clusters=GO:0001826!inner cell mass cell differentiation!0.00977232251375934!54475$GO:0001825!blastocyst formation!0.00977232251375934!54475$GO:0006432!phenylalanyl-tRNA aminoacylation!0.0146558949108512!2193$GO:0004826!phenylalanine-tRNA ligase activity!0.0146558949108512!2193$GO:0001824!blastocyst development!0.0273480076998137!54475
|gostat_on_coexpression_clusters=GO:0001826!inner cell mass cell differentiation!0.00977232251375934!54475$GO:0001825!blastocyst formation!0.00977232251375934!54475$GO:0006432!phenylalanyl-tRNA aminoacylation!0.0146558949108512!2193$GO:0004826!phenylalanine-tRNA ligase activity!0.0146558949108512!2193$GO:0001824!blastocyst development!0.0273480076998137!54475
|id=C2400
|id=C2400
|ontology_enrichment_celltype=CL:0000548!1.08e-26!679;CL:0000004!1.08e-26!679;CL:0000255!1.08e-26!679;CL:0000012!1.15e-26!682;CL:0000066!5.76e-24!254;CL:0002321!4.33e-21!248;CL:0000220!1.86e-20!246;CL:0000003!2.29e-16!722;CL:0000144!1.02e-13!625;CL:0000222!2.24e-12!119;CL:0002371!7.22e-10!591;CL:0000055!1.37e-09!180;CL:0000063!3.10e-09!578;CL:0000076!7.26e-09!62;CL:0000183!1.40e-08!59;CL:0000393!1.37e-07!60;CL:0000211!1.37e-07!60;CL:0000187!6.10e-07!54;CL:0000680!9.37e-07!57;CL:0000056!9.37e-07!57;CL:0000355!9.37e-07!57
|ontology_enrichment_disease=DOID:162!2.88e-21!235;DOID:14566!9.39e-21!239;DOID:2531!1.00e-15!51;DOID:0060083!1.00e-15!51;DOID:1240!9.78e-14!39;DOID:8692!2.64e-12!31;DOID:0050686!1.18e-11!137;DOID:0050687!5.00e-09!143;DOID:305!4.53e-08!106
|ontology_enrichment_uberon=UBERON:0003104!4.53e-12!238;UBERON:0009142!4.53e-12!238;UBERON:0003914!4.32e-10!118;UBERON:0000490!3.03e-09!138;UBERON:0000486!1.82e-08!82;UBERON:0002100!3.58e-08!216;UBERON:0000055!5.02e-08!69;UBERON:0002049!7.51e-08!79;UBERON:0007798!7.51e-08!79;UBERON:0004290!8.61e-08!70;UBERON:0001981!9.03e-08!60;UBERON:0007500!9.03e-08!60;UBERON:0004537!9.03e-08!60;UBERON:0006965!9.03e-08!60;UBERON:0005256!1.16e-07!143;UBERON:0001637!1.49e-07!42;UBERON:0003509!1.49e-07!42;UBERON:0004572!1.49e-07!42;UBERON:0000072!1.54e-07!46;UBERON:0004872!2.14e-07!84;UBERON:0001048!4.16e-07!168;UBERON:0008947!5.61e-07!38;UBERON:0003258!5.61e-07!38;UBERON:0000487!8.87e-07!22
}}
}}

Revision as of 14:23, 21 May 2012


Full id: C2400_Alveolar_embryonic_Mesenchymal_Renal_Smooth_acute_granulocyte



Phase1 CAGE Peaks

Hg19::chr17:33469299..33469328,-p1@NLE1
Hg19::chr19:13044513..13044543,-p1@FARSA
Hg19::chr19:48949218..48949267,+p1@GRWD1
Hg19::chr19:56166360..56166452,+p1@U2AF2


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:0001826inner cell mass cell differentiation0.00977232251375934
GO:0001825blastocyst formation0.00977232251375934
GO:0006432phenylalanyl-tRNA aminoacylation0.0146558949108512
GO:0004826phenylalanine-tRNA ligase activity0.0146558949108512
GO:0001824blastocyst development0.0273480076998137



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
animal cell1.08e-26679
eukaryotic cell1.08e-26679
epithelial cell5.76e-24254
embryonic cell4.33e-21248
native cell2.29e-16722
mesodermal cell2.24e-12119
somatic cell7.22e-10591
non-terminally differentiated cell1.37e-09180
squamous epithelial cell7.26e-0962
contractile cell1.40e-0859
electrically responsive cell1.37e-0760
electrically active cell1.37e-0760
muscle cell6.10e-0754
muscle precursor cell9.37e-0757
myoblast9.37e-0757
multi-potent skeletal muscle stem cell9.37e-0757
Uber Anatomy
Ontology termp-valuen
mesenchyme4.53e-12238
entire embryonic mesenchyme4.53e-12238
epithelial tube4.32e-10118
unilaminar epithelium3.03e-09138
multilaminar epithelium1.82e-0882
trunk3.58e-08216
vessel5.02e-0869
vasculature7.51e-0879
vascular system7.51e-0879
dermomyotome8.61e-0870
blood vessel9.03e-0860
epithelial tube open at both ends9.03e-0860
blood vasculature9.03e-0860
vascular cord9.03e-0860
trunk mesenchyme1.16e-07143
artery1.49e-0742
arterial blood vessel1.49e-0742
arterial system1.49e-0742
segment of respiratory tract1.54e-0746
splanchnic layer of lateral plate mesoderm2.14e-0784
primordium4.16e-07168
respiratory primordium5.61e-0738
endoderm of foregut5.61e-0738
simple squamous epithelium8.87e-0722
Disease
Ontology termp-valuen
cancer2.88e-21235
disease of cellular proliferation9.39e-21239
hematologic cancer1.00e-1551
immune system cancer1.00e-1551
leukemia9.78e-1439
myeloid leukemia2.64e-1231
organ system cancer1.18e-11137
cell type cancer5.00e-09143
carcinoma4.53e-08106


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)

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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


No analysis results for this cluster

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.