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|full_id=C1472_nonsmall_neuroblastoma_small_tubular_carcinoid_smallcell_merkel
|full_id=C1472_nonsmall_neuroblastoma_small_tubular_carcinoid_smallcell_merkel
|id=C1472
|id=C1472
|ontology_enrichment_celltype=CL:0002319!6.31e-11!25
|ontology_enrichment_disease=DOID:0050687!5.00e-16!143;DOID:162!1.68e-11!235;DOID:14566!8.63e-11!239;DOID:305!3.69e-10!106;DOID:3095!3.40e-07!22;DOID:2994!3.40e-07!22
|ontology_enrichment_uberon=UBERON:0000073!8.02e-37!94;UBERON:0001016!8.02e-37!94;UBERON:0005743!8.86e-35!86;UBERON:0001017!2.07e-34!82;UBERON:0000955!3.53e-27!69;UBERON:0006238!3.53e-27!69;UBERON:0001049!8.36e-26!57;UBERON:0005068!8.36e-26!57;UBERON:0006241!8.36e-26!57;UBERON:0007135!8.36e-26!57;UBERON:0002346!2.74e-24!90;UBERON:0002616!1.19e-22!59;UBERON:0003075!1.51e-22!86;UBERON:0007284!1.51e-22!86;UBERON:0000924!2.89e-22!173;UBERON:0006601!2.89e-22!173;UBERON:0004121!9.99e-21!169;UBERON:0002780!2.05e-20!41;UBERON:0001890!2.05e-20!41;UBERON:0006240!2.05e-20!41;UBERON:0003080!2.29e-19!42;UBERON:0000153!3.68e-18!129;UBERON:0007811!3.68e-18!129;UBERON:0002020!9.76e-18!34;UBERON:0003528!9.76e-18!34;UBERON:0000033!1.10e-17!123;UBERON:0001893!1.13e-17!34;UBERON:0002791!3.77e-17!33;UBERON:0001869!5.04e-17!32;UBERON:0003056!1.07e-16!61;UBERON:0000956!2.22e-13!25;UBERON:0000203!2.22e-13!25;UBERON:0007023!8.66e-13!115;UBERON:0002619!3.48e-12!22;UBERON:0001950!1.98e-11!20;UBERON:0000062!1.09e-09!511;UBERON:0000064!1.24e-09!219;UBERON:0000922!4.20e-08!612;UBERON:0003076!1.30e-07!15;UBERON:0003057!1.30e-07!15
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Revision as of 14:12, 21 May 2012


Full id: C1472_nonsmall_neuroblastoma_small_tubular_carcinoid_smallcell_merkel



Phase1 CAGE Peaks

Hg19::chr1:235813008..235813019,-p8@GNG4
Hg19::chr1:235813034..235813097,-p1@GNG4
Hg19::chr1:235813117..235813120,-p11@GNG4
Hg19::chr1:235813272..235813285,-p6@GNG4
Hg19::chr1:235813290..235813323,-p2@GNG4
Hg19::chr1:235813325..235813360,-p3@GNG4


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
neural cell6.31e-1125
Uber Anatomy
Ontology termp-valuen
regional part of nervous system8.02e-3794
nervous system8.02e-3794
central nervous system2.07e-3482
brain3.53e-2769
future brain3.53e-2769
neural tube8.36e-2657
neural rod8.36e-2657
future spinal cord8.36e-2657
neural keel8.36e-2657
neurectoderm2.74e-2490
regional part of brain1.19e-2259
neural plate1.51e-2286
presumptive neural plate1.51e-2286
ectoderm2.89e-22173
presumptive ectoderm2.89e-22173
ectoderm-derived structure9.99e-21169
regional part of forebrain2.05e-2041
forebrain2.05e-2041
future forebrain2.05e-2041
anterior neural tube2.29e-1942
anterior region of body3.68e-18129
craniocervical region3.68e-18129
gray matter9.76e-1834
brain grey matter9.76e-1834
head1.10e-17123
telencephalon1.13e-1734
regional part of telencephalon3.77e-1733
cerebral hemisphere5.04e-1732
pre-chordal neural plate1.07e-1661
cerebral cortex2.22e-1325
pallium2.22e-1325
adult organism8.66e-13115
regional part of cerebral cortex3.48e-1222
neocortex1.98e-1120
organ1.09e-09511
organ part1.24e-09219
embryo4.20e-08612
posterior neural tube1.30e-0715
chordal neural plate1.30e-0715
Disease
Ontology termp-valuen
cell type cancer5.00e-16143
cancer1.68e-11235
disease of cellular proliferation8.63e-11239
carcinoma3.69e-10106
germ cell and embryonal cancer3.40e-0722
germ cell cancer3.40e-0722


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


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.