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Coexpression cluster:C402

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Full id: C402_parietal_occipital_temporal_thalamus_optic_globus_brain



Phase1 CAGE Peaks

Hg19::chr12:123319068..123319080,+p6@HIP1R
Hg19::chr14:32799950..32799951,+p@chr14:32799950..32799951
+
Hg19::chr19:11562361..11562386,-p@chr19:11562361..11562386
-
Hg19::chr19:13134043..13134054,+p@chr19:13134043..13134054
+
Hg19::chr19:47142400..47142423,-p1@uc002pez.1
Hg19::chr19:55946892..55946910,-p@chr19:55946892..55946910
-
Hg19::chr1:172051480..172051484,+p@chr1:172051480..172051484
+
Hg19::chr20:58279639..58279642,+p@chr20:58279639..58279642
+
Hg19::chr21:41551108..41551112,-p@chr21:41551108..41551112
-
Hg19::chr22:18503369..18503380,-p@chr22:18503369..18503380
-
Hg19::chr3:181442608..181442615,+p@chr3:181442608..181442615
+
Hg19::chr4:113994134..113994138,+p@chr4:113994134..113994138
+
Hg19::chr4:114286837..114286840,+p@chr4:114286837..114286840
+
Hg19::chr4:164928140..164928142,-p@chr4:164928140..164928142
-
Hg19::chr4:164948511..164948515,-p@chr4:164948511..164948515
-
Hg19::chr4:165244747..165244750,-p@chr4:165244747..165244750
-
Hg19::chr5:146146606..146146609,-p@chr5:146146606..146146609
-
Hg19::chr5:146243956..146243960,-p@chr5:146243956..146243960
-
Hg19::chr7:86415034..86415036,+p@chr7:86415034..86415036
+
Hg19::chr9:103281957..103281962,+p@chr9:103281957..103281962
+
Hg19::chr9:8463305..8463309,-p@chr9:8463305..8463309
-
Hg19::chr9:8491655..8491659,-p@chr9:8491655..8491659
-
Hg19::chr9:8500547..8500558,-p@chr9:8500547..8500558
-
Hg19::chr9:8576629..8576632,-p@chr9:8576629..8576632
-
Hg19::chr9:8858623..8858638,-p@chr9:8858623..8858638
-
Hg19::chrX:13904834..13904839,-p@chrX:13904834..13904839
-


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:0005905coated pit0.0316437065818909
GO:0030136clathrin-coated vesicle0.0358138074492719
GO:0030135coated vesicle0.0358138074492719
GO:0005543phospholipid binding0.0358138074492719
GO:0016023cytoplasmic membrane-bound vesicle0.0358138074492719
GO:0031988membrane-bound vesicle0.0358138074492719
GO:0031410cytoplasmic vesicle0.0358138074492719
GO:0031982vesicle0.0358138074492719
GO:0003779actin binding0.0358138074492719
GO:0008289lipid binding0.0403407083908673
GO:0008092cytoskeletal protein binding0.0403407083908673



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
neural cell6.90e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system1.96e-3582
regional part of nervous system3.40e-3594
nervous system3.40e-3594
neural tube1.20e-3357
neural rod1.20e-3357
future spinal cord1.20e-3357
neural keel1.20e-3357
adult organism7.83e-29115
brain1.15e-2869
future brain1.15e-2869
neurectoderm1.36e-2790
regional part of brain1.00e-2659
regional part of forebrain1.03e-2641
forebrain1.03e-2641
future forebrain1.03e-2641
anterior neural tube2.37e-2642
neural plate5.69e-2686
presumptive neural plate5.69e-2686
gray matter1.01e-2234
brain grey matter1.01e-2234
telencephalon1.14e-2234
regional part of telencephalon4.32e-2233
ectoderm1.66e-21173
presumptive ectoderm1.66e-21173
cerebral hemisphere2.45e-2132
ectoderm-derived structure4.14e-20169
pre-chordal neural plate2.13e-1761
cerebral cortex5.36e-1725
pallium5.36e-1725
anterior region of body1.31e-16129
craniocervical region1.31e-16129
head2.43e-16123
regional part of cerebral cortex1.13e-1522
neocortex2.14e-1420
posterior neural tube2.05e-0815
chordal neural plate2.05e-0815
segmental subdivision of nervous system2.95e-0713
nucleus of brain3.56e-079
neural nucleus3.56e-079
basal ganglion3.68e-079
nuclear complex of neuraxis3.68e-079
aggregate regional part of brain3.68e-079
collection of basal ganglia3.68e-079
cerebral subcortex3.68e-079


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.