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Coexpression cluster:C1229

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Full id: C1229_cerebellum_occipital_parietal_pineal_middle_medial_amygdala



Phase1 CAGE Peaks

Hg19::chr17:5095351..5095419,+p1@LOC100130950
Hg19::chr19:37998036..37998098,+p2@ZNF793
Hg19::chr19:52839515..52839572,+p1@ZNF610
Hg19::chr19:57988878..57988941,-p1@ZNF772
Hg19::chr1:200708012..200708074,+p@chr1:200708012..200708074
+
Hg19::chr5:178322893..178322931,+p1@ZFP2
Hg19::chr5:178368186..178368238,+p1@ZNF454


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


p.valueFDRnGenesnPathwayName
2.75303467843507e-091.7426709514494e-065390{ASH2L,391} (Static Module):NA



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:0006355regulation of transcription, DNA-dependent7.7530361604906e-05
GO:0006351transcription, DNA-dependent7.7530361604906e-05
GO:0032774RNA biosynthetic process7.7530361604906e-05
GO:0003677DNA binding7.7530361604906e-05
GO:0045449regulation of transcription7.7530361604906e-05
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process7.7530361604906e-05
GO:0006350transcription7.7530361604906e-05
GO:0010468regulation of gene expression7.7530361604906e-05
GO:0031323regulation of cellular metabolic process7.78470640173588e-05
GO:0019222regulation of metabolic process7.78470640173588e-05
GO:0016070RNA metabolic process7.78470640173588e-05
GO:0008270zinc ion binding7.78470640173588e-05
GO:0046914transition metal ion binding0.000163152953123399
GO:0010467gene expression0.00025861416676931
GO:0050794regulation of cellular process0.000302027107601188
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000320756298776466
GO:0005634nucleus0.00036014843875417
GO:0050789regulation of biological process0.000363800291165466
GO:0003676nucleic acid binding0.000416532099838324
GO:0043169cation binding0.000434377092938975
GO:0065007biological regulation0.000493781123385218
GO:0046872metal ion binding0.000511515697461135
GO:0043167ion binding0.000532195466049185
GO:0043283biopolymer metabolic process0.000987064155825241
GO:0043231intracellular membrane-bound organelle0.00154739567627646
GO:0043227membrane-bound organelle0.00154739567627646
GO:0043229intracellular organelle0.00388253171397565
GO:0043226organelle0.00388253171397565
GO:0043170macromolecule metabolic process0.00445060385533282
GO:0044237cellular metabolic process0.00816727793047431
GO:0044238primary metabolic process0.00820792120921185
GO:0044424intracellular part0.00857444245426504
GO:0005622intracellular0.0167494844650136



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.86e-4094
nervous system1.86e-4094
ectoderm6.64e-38173
presumptive ectoderm6.64e-38173
central nervous system1.19e-3782
ectoderm-derived structure2.44e-37169
neural tube5.24e-3457
neural rod5.24e-3457
future spinal cord5.24e-3457
neural keel5.24e-3457
adult organism2.67e-33115
regional part of brain2.87e-3259
neurectoderm3.78e-3290
neural plate6.54e-3286
presumptive neural plate6.54e-3286
brain8.52e-3269
future brain8.52e-3269
head2.88e-30123
anterior region of body1.01e-29129
craniocervical region1.01e-29129
anterior neural tube6.62e-2742
regional part of forebrain1.07e-2641
forebrain1.07e-2641
future forebrain1.07e-2641
organism subdivision2.37e-26365
pre-chordal neural plate3.34e-2461
telencephalon3.20e-2234
gray matter3.35e-2234
brain grey matter3.35e-2234
regional part of telencephalon1.34e-2133
cerebral hemisphere4.47e-2132
multi-cellular organism1.58e-18659
multi-tissue structure5.32e-18347
cerebral cortex9.82e-1725
pallium9.82e-1725
regional part of cerebral cortex1.27e-1522
neocortex2.37e-1420
epithelium1.09e-13309
cell layer1.14e-13312
anatomical cluster1.09e-12286
embryo1.89e-12612
anatomical system2.36e-12625
anatomical conduit2.49e-12241
anatomical group3.18e-12626
organ3.80e-12511
organ part4.23e-12219
embryonic structure2.19e-10605
developing anatomical structure2.19e-10605
tube2.37e-10194
germ layer4.33e-10604
embryonic tissue4.33e-10604
presumptive structure4.33e-10604
epiblast (generic)4.33e-10604
posterior neural tube3.01e-0815
chordal neural plate3.01e-0815
segmental subdivision of nervous system4.26e-0713
basal ganglion4.57e-079
nuclear complex of neuraxis4.57e-079
aggregate regional part of brain4.57e-079
collection of basal ganglia4.57e-079
cerebral subcortex4.57e-079
nucleus of brain6.45e-079
neural nucleus6.45e-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.