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Coexpression cluster:C561: Difference between revisions

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|ontology_enrichment_disease=DOID:3095!7.70e-08!22;DOID:2994!7.70e-08!22
|ontology_enrichment_disease=DOID:3095!7.70e-08!22;DOID:2994!7.70e-08!22
|ontology_enrichment_uberon=UBERON:0000073!9.48e-46!94;UBERON:0001016!9.48e-46!94;UBERON:0005743!1.10e-44!86;UBERON:0001017!2.73e-44!82;UBERON:0000955!4.32e-36!69;UBERON:0006238!4.32e-36!69;UBERON:0001049!3.78e-34!57;UBERON:0005068!3.78e-34!57;UBERON:0006241!3.78e-34!57;UBERON:0007135!3.78e-34!57;UBERON:0002616!5.13e-32!59;UBERON:0002346!2.05e-31!90;UBERON:0003075!1.03e-29!86;UBERON:0007284!1.03e-29!86;UBERON:0000924!1.01e-25!173;UBERON:0006601!1.01e-25!173;UBERON:0003080!1.85e-25!42;UBERON:0002780!1.98e-25!41;UBERON:0001890!1.98e-25!41;UBERON:0006240!1.98e-25!41;UBERON:0004121!3.42e-24!169;UBERON:0003056!2.07e-22!61;UBERON:0001893!2.26e-22!34;UBERON:0002020!2.58e-22!34;UBERON:0003528!2.58e-22!34;UBERON:0002791!1.01e-21!33;UBERON:0001869!3.14e-21!32;UBERON:0000033!4.71e-21!123;UBERON:0000153!1.94e-20!129;UBERON:0007811!1.94e-20!129;UBERON:0007023!3.03e-20!115;UBERON:0000956!5.65e-17!25;UBERON:0000203!5.65e-17!25;UBERON:0002619!2.78e-15!22;UBERON:0001950!4.82e-14!20;UBERON:0003076!1.03e-09!15;UBERON:0003057!1.03e-09!15;UBERON:0004732!1.88e-08!13;UBERON:0004733!5.88e-08!12;UBERON:0002028!5.88e-08!12;UBERON:0007277!5.88e-08!12;UBERON:0000062!9.59e-08!511;UBERON:0002420!6.84e-07!9;UBERON:0007245!6.84e-07!9;UBERON:0010009!6.84e-07!9;UBERON:0010011!6.84e-07!9;UBERON:0000454!6.84e-07!9;UBERON:0002308!8.66e-07!9;UBERON:0000125!8.66e-07!9
|ontology_enrichment_uberon=UBERON:0000073!9.48e-46!94;UBERON:0001016!9.48e-46!94;UBERON:0005743!1.10e-44!86;UBERON:0001017!2.73e-44!82;UBERON:0000955!4.32e-36!69;UBERON:0006238!4.32e-36!69;UBERON:0001049!3.78e-34!57;UBERON:0005068!3.78e-34!57;UBERON:0006241!3.78e-34!57;UBERON:0007135!3.78e-34!57;UBERON:0002616!5.13e-32!59;UBERON:0002346!2.05e-31!90;UBERON:0003075!1.03e-29!86;UBERON:0007284!1.03e-29!86;UBERON:0000924!1.01e-25!173;UBERON:0006601!1.01e-25!173;UBERON:0003080!1.85e-25!42;UBERON:0002780!1.98e-25!41;UBERON:0001890!1.98e-25!41;UBERON:0006240!1.98e-25!41;UBERON:0004121!3.42e-24!169;UBERON:0003056!2.07e-22!61;UBERON:0001893!2.26e-22!34;UBERON:0002020!2.58e-22!34;UBERON:0003528!2.58e-22!34;UBERON:0002791!1.01e-21!33;UBERON:0001869!3.14e-21!32;UBERON:0000033!4.71e-21!123;UBERON:0000153!1.94e-20!129;UBERON:0007811!1.94e-20!129;UBERON:0007023!3.03e-20!115;UBERON:0000956!5.65e-17!25;UBERON:0000203!5.65e-17!25;UBERON:0002619!2.78e-15!22;UBERON:0001950!4.82e-14!20;UBERON:0003076!1.03e-09!15;UBERON:0003057!1.03e-09!15;UBERON:0004732!1.88e-08!13;UBERON:0004733!5.88e-08!12;UBERON:0002028!5.88e-08!12;UBERON:0007277!5.88e-08!12;UBERON:0000062!9.59e-08!511;UBERON:0002420!6.84e-07!9;UBERON:0007245!6.84e-07!9;UBERON:0010009!6.84e-07!9;UBERON:0010011!6.84e-07!9;UBERON:0000454!6.84e-07!9;UBERON:0002308!8.66e-07!9;UBERON:0000125!8.66e-07!9
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}}
}}

Revision as of 20:31, 8 August 2012


Full id: C561_brain_Neural_spinal_Neurons_parietal_temporal_occipital



Phase1 CAGE Peaks

Hg19::chr11:65816664..65816675,-p2@GAL3ST3
Hg19::chr13:36705425..36705445,-p5@DCLK1
Hg19::chr13:53422767..53422780,-p1@PCDH8
Hg19::chr19:19322758..19322773,+p1@NCAN
Hg19::chr19:19322805..19322812,+p2@NCAN
Hg19::chr1:156391550..156391569,-p2@C1orf61
Hg19::chr1:156399211..156399225,-p1@C1orf61
Hg19::chr1:156400037..156400063,-p@chr1:156400037..156400063
-
Hg19::chr22:42372970..42372971,+p5@SEPT3
Hg19::chr2:26395939..26396015,+p2@FAM59B
Hg19::chr3:26664252..26664268,+p5@LRRC3B
Hg19::chr3:65387362..65387385,-p14@MAGI1
Hg19::chr4:150999554..150999573,+p6@DCLK2
Hg19::chr5:140787600..140787637,+p2@PCDHGB6
Hg19::chr5:87968909..87968913,-p2@LINC00461
Hg19::chr5:87969130..87969153,-p1@LINC00461


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:0022610biological adhesion0.00364590195774595
GO:0007155cell adhesion0.00364590195774595
GO:0016337cell-cell adhesion0.00364590195774595
GO:0050698proteoglycan sulfotransferase activity0.0170795551236903
GO:0030309poly-N-acetyllactosamine metabolic process0.0170795551236903
GO:0050694galactose 3-O-sulfotransferase activity0.0170795551236903
GO:0001733galactosylceramide sulfotransferase activity0.0170795551236903
GO:0017076purine nucleotide binding0.0170795551236903
GO:0007156homophilic cell adhesion0.0170795551236903
GO:00506563'-phosphoadenosine 5'-phosphosulfate binding0.0170795551236903
GO:0007158neuron adhesion0.0217324972662446
GO:0000166nucleotide binding0.0271439940753673
GO:0030554adenyl nucleotide binding0.0468748694812944
GO:0030166proteoglycan biosynthetic process0.0468748694812944
GO:0005509calcium ion binding0.0468748694812944
GO:0009311oligosaccharide metabolic process0.0468748694812944



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 cell5.18e-1025
neurectodermal cell2.13e-0859
Uber Anatomy
Ontology termp-valuen
regional part of nervous system9.48e-4694
nervous system9.48e-4694
central nervous system2.73e-4482
brain4.32e-3669
future brain4.32e-3669
neural tube3.78e-3457
neural rod3.78e-3457
future spinal cord3.78e-3457
neural keel3.78e-3457
regional part of brain5.13e-3259
neurectoderm2.05e-3190
neural plate1.03e-2986
presumptive neural plate1.03e-2986
ectoderm1.01e-25173
presumptive ectoderm1.01e-25173
anterior neural tube1.85e-2542
regional part of forebrain1.98e-2541
forebrain1.98e-2541
future forebrain1.98e-2541
ectoderm-derived structure3.42e-24169
pre-chordal neural plate2.07e-2261
telencephalon2.26e-2234
gray matter2.58e-2234
brain grey matter2.58e-2234
regional part of telencephalon1.01e-2133
cerebral hemisphere3.14e-2132
head4.71e-21123
anterior region of body1.94e-20129
craniocervical region1.94e-20129
adult organism3.03e-20115
cerebral cortex5.65e-1725
pallium5.65e-1725
regional part of cerebral cortex2.78e-1522
neocortex4.82e-1420
posterior neural tube1.03e-0915
chordal neural plate1.03e-0915
segmental subdivision of nervous system1.88e-0813
segmental subdivision of hindbrain5.88e-0812
hindbrain5.88e-0812
presumptive hindbrain5.88e-0812
organ9.59e-08511
basal ganglion6.84e-079
nuclear complex of neuraxis6.84e-079
aggregate regional part of brain6.84e-079
collection of basal ganglia6.84e-079
cerebral subcortex6.84e-079
nucleus of brain8.66e-079
neural nucleus8.66e-079
Disease
Ontology termp-valuen
germ cell and embryonal cancer7.70e-0822
germ cell cancer7.70e-0822


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.