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Coexpression cluster:C3018: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.05e-38!115;UBERON:0001049!1.36e-29!57;UBERON:0005068!1.36e-29!57;UBERON:0006241!1.36e-29!57;UBERON:0007135!1.36e-29!57;UBERON:0002616!1.44e-25!59;UBERON:0003080!8.39e-25!42;UBERON:0002780!3.09e-24!41;UBERON:0001890!3.09e-24!41;UBERON:0006240!3.09e-24!41;UBERON:0001017!5.31e-23!82;UBERON:0003075!6.52e-23!86;UBERON:0007284!6.52e-23!86;UBERON:0000955!3.20e-22!69;UBERON:0006238!3.20e-22!69;UBERON:0002346!3.71e-22!90;UBERON:0005743!9.08e-22!86;UBERON:0001893!2.02e-20!34;UBERON:0002020!2.39e-20!34;UBERON:0003528!2.39e-20!34;UBERON:0000468!3.32e-20!659;UBERON:0000062!5.29e-20!511;UBERON:0002791!8.14e-20!33;UBERON:0001869!3.35e-19!32;UBERON:0000073!5.30e-19!94;UBERON:0001016!5.30e-19!94;UBERON:0000467!4.16e-18!625;UBERON:0000480!1.07e-17!626;UBERON:0004121!4.76e-17!169;UBERON:0000924!7.87e-17!173;UBERON:0006601!7.87e-17!173;UBERON:0000033!1.69e-16!123;UBERON:0003056!1.74e-16!61;UBERON:0000153!9.49e-16!129;UBERON:0007811!9.49e-16!129;UBERON:0002619!2.44e-15!22;UBERON:0000956!9.81e-15!25;UBERON:0000203!9.81e-15!25;UBERON:0001950!3.75e-14!20;UBERON:0000922!2.80e-13!612;UBERON:0002050!1.30e-12!605;UBERON:0005423!1.30e-12!605;UBERON:0000475!1.74e-12!365;UBERON:0000923!2.66e-12!604;UBERON:0005291!2.66e-12!604;UBERON:0006598!2.66e-12!604;UBERON:0002532!2.66e-12!604;UBERON:0004111!2.44e-09!241;UBERON:0000025!3.05e-08!194;UBERON:0002420!3.72e-07!9;UBERON:0007245!3.72e-07!9;UBERON:0010009!3.72e-07!9;UBERON:0010011!3.72e-07!9;UBERON:0000454!3.72e-07!9;UBERON:0002308!4.11e-07!9;UBERON:0000125!4.11e-07!9;UBERON:0000477!8.95e-07!286
|ontology_enrichment_uberon=UBERON:0007023!2.05e-38!115;UBERON:0001049!1.36e-29!57;UBERON:0005068!1.36e-29!57;UBERON:0006241!1.36e-29!57;UBERON:0007135!1.36e-29!57;UBERON:0002616!1.44e-25!59;UBERON:0003080!8.39e-25!42;UBERON:0002780!3.09e-24!41;UBERON:0001890!3.09e-24!41;UBERON:0006240!3.09e-24!41;UBERON:0001017!5.31e-23!82;UBERON:0003075!6.52e-23!86;UBERON:0007284!6.52e-23!86;UBERON:0000955!3.20e-22!69;UBERON:0006238!3.20e-22!69;UBERON:0002346!3.71e-22!90;UBERON:0005743!9.08e-22!86;UBERON:0001893!2.02e-20!34;UBERON:0002020!2.39e-20!34;UBERON:0003528!2.39e-20!34;UBERON:0000468!3.32e-20!659;UBERON:0000062!5.29e-20!511;UBERON:0002791!8.14e-20!33;UBERON:0001869!3.35e-19!32;UBERON:0000073!5.30e-19!94;UBERON:0001016!5.30e-19!94;UBERON:0000467!4.16e-18!625;UBERON:0000480!1.07e-17!626;UBERON:0004121!4.76e-17!169;UBERON:0000924!7.87e-17!173;UBERON:0006601!7.87e-17!173;UBERON:0000033!1.69e-16!123;UBERON:0003056!1.74e-16!61;UBERON:0000153!9.49e-16!129;UBERON:0007811!9.49e-16!129;UBERON:0002619!2.44e-15!22;UBERON:0000956!9.81e-15!25;UBERON:0000203!9.81e-15!25;UBERON:0001950!3.75e-14!20;UBERON:0000922!2.80e-13!612;UBERON:0002050!1.30e-12!605;UBERON:0005423!1.30e-12!605;UBERON:0000475!1.74e-12!365;UBERON:0000923!2.66e-12!604;UBERON:0005291!2.66e-12!604;UBERON:0006598!2.66e-12!604;UBERON:0002532!2.66e-12!604;UBERON:0004111!2.44e-09!241;UBERON:0000025!3.05e-08!194;UBERON:0002420!3.72e-07!9;UBERON:0007245!3.72e-07!9;UBERON:0010009!3.72e-07!9;UBERON:0010011!3.72e-07!9;UBERON:0000454!3.72e-07!9;UBERON:0002308!4.11e-07!9;UBERON:0000125!4.11e-07!9;UBERON:0000477!8.95e-07!286
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}}
}}

Revision as of 18:50, 8 August 2012


Full id: C3018_optic_cerebellum_globus_caudate_occipital_hippocampus_medial



Phase1 CAGE Peaks

Hg19::chr10:45455081..45455101,-p2@TMEM72-AS1
Hg19::chr20:3388541..3388575,-p2@C20orf194
Hg19::chr20:3388579..3388619,-p3@C20orf194


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><br>

Cell Type
Ontology termp-valuen
CD14-positive, CD16-negative classical monocyte5.85e-0842
Uber Anatomy
Ontology termp-valuen
adult organism2.05e-38115
neural tube1.36e-2957
neural rod1.36e-2957
future spinal cord1.36e-2957
neural keel1.36e-2957
regional part of brain1.44e-2559
anterior neural tube8.39e-2542
regional part of forebrain3.09e-2441
forebrain3.09e-2441
future forebrain3.09e-2441
central nervous system5.31e-2382
neural plate6.52e-2386
presumptive neural plate6.52e-2386
brain3.20e-2269
future brain3.20e-2269
neurectoderm3.71e-2290
telencephalon2.02e-2034
gray matter2.39e-2034
brain grey matter2.39e-2034
multi-cellular organism3.32e-20659
organ5.29e-20511
regional part of telencephalon8.14e-2033
cerebral hemisphere3.35e-1932
regional part of nervous system5.30e-1994
nervous system5.30e-1994
anatomical system4.16e-18625
anatomical group1.07e-17626
ectoderm-derived structure4.76e-17169
ectoderm7.87e-17173
presumptive ectoderm7.87e-17173
head1.69e-16123
pre-chordal neural plate1.74e-1661
anterior region of body9.49e-16129
craniocervical region9.49e-16129
regional part of cerebral cortex2.44e-1522
cerebral cortex9.81e-1525
pallium9.81e-1525
neocortex3.75e-1420
embryo2.80e-13612
embryonic structure1.30e-12605
developing anatomical structure1.30e-12605
organism subdivision1.74e-12365
germ layer2.66e-12604
embryonic tissue2.66e-12604
presumptive structure2.66e-12604
epiblast (generic)2.66e-12604
anatomical conduit2.44e-09241
tube3.05e-08194
basal ganglion3.72e-079
nuclear complex of neuraxis3.72e-079
aggregate regional part of brain3.72e-079
collection of basal ganglia3.72e-079
cerebral subcortex3.72e-079
nucleus of brain4.11e-079
neural nucleus4.11e-079
anatomical cluster8.95e-07286


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.

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