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|gostat_on_coexpression_clusters=GO:0005118!sevenless binding!0.0121861478021528!51704
|gostat_on_coexpression_clusters=GO:0005118!sevenless binding!0.0121861478021528!51704
|id=C1135
|id=C1135
|ontology_enrichment_celltype=CL:0000213!7.56e-09!57;CL:0000215!7.56e-09!57;CL:0000222!8.91e-09!119;CL:0000077!2.68e-07!19
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!6.46e-36!82;UBERON:0001049!3.66e-35!57;UBERON:0005068!3.66e-35!57;UBERON:0006241!3.66e-35!57;UBERON:0007135!3.66e-35!57;UBERON:0005743!5.45e-35!86;UBERON:0000073!2.82e-30!94;UBERON:0001016!2.82e-30!94;UBERON:0004111!3.04e-30!241;UBERON:0003075!7.79e-30!86;UBERON:0007284!7.79e-30!86;UBERON:0000955!1.34e-29!69;UBERON:0006238!1.34e-29!69;UBERON:0007023!1.57e-29!115;UBERON:0002616!5.94e-29!59;UBERON:0002346!5.26e-27!90;UBERON:0000025!1.87e-26!194;UBERON:0003080!2.42e-25!42;UBERON:0002780!5.30e-25!41;UBERON:0001890!5.30e-25!41;UBERON:0006240!5.30e-25!41;UBERON:0000477!1.65e-24!286;UBERON:0002020!4.80e-22!34;UBERON:0003528!4.80e-22!34;UBERON:0001893!5.92e-22!34;UBERON:0000483!2.45e-21!309;UBERON:0002791!2.89e-21!33;UBERON:0000119!7.06e-21!312;UBERON:0001869!2.37e-20!32;UBERON:0004121!3.90e-18!169;UBERON:0003056!3.29e-17!61;UBERON:0000153!5.20e-17!129;UBERON:0007811!5.20e-17!129;UBERON:0000033!6.29e-17!123;UBERON:0000924!7.88e-17!173;UBERON:0006601!7.88e-17!173;UBERON:0000956!2.71e-15!25;UBERON:0000203!2.71e-15!25;UBERON:0002619!1.25e-13!22;UBERON:0001950!2.11e-12!20;UBERON:0000475!1.43e-11!365;UBERON:0003076!7.83e-11!15;UBERON:0003057!7.83e-11!15;UBERON:0000481!1.29e-10!347;UBERON:0000468!5.78e-10!659;UBERON:0004732!3.11e-09!13;UBERON:0000467!5.84e-09!625;UBERON:0000480!8.02e-09!626;UBERON:0004733!1.52e-08!12;UBERON:0002028!1.52e-08!12;UBERON:0007277!1.52e-08!12;UBERON:0002308!2.44e-08!9;UBERON:0000125!2.44e-08!9;UBERON:0000922!2.68e-08!612;UBERON:0002420!3.84e-08!9;UBERON:0007245!3.84e-08!9;UBERON:0010009!3.84e-08!9;UBERON:0010011!3.84e-08!9;UBERON:0000454!3.84e-08!9;UBERON:0000064!4.74e-08!219;UBERON:0003103!3.02e-07!69;UBERON:0003914!3.47e-07!118;UBERON:0002298!4.22e-07!8;UBERON:0000062!7.83e-07!511;UBERON:0009663!8.46e-07!7
}}
}}

Revision as of 14:07, 21 May 2012


Full id: C1135_hippocampus_substantia_thalamus_occipital_locus_medial_brain



Phase1 CAGE Peaks

Hg19::chr11:124793774..124793796,-p10@HEPACAM
Hg19::chr16:19869963..19870000,-p@chr16:19869963..19870000
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Hg19::chr16:19871670..19871687,-p@chr16:19871670..19871687
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Hg19::chr16:19871741..19871755,-p@chr16:19871741..19871755
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Hg19::chr16:19873226..19873239,-p3@GPRC5B
Hg19::chr16:19883175..19883186,-p@chr16:19883175..19883186
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Hg19::chr16:19883313..19883333,-p@chr16:19883313..19883333
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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:0005118sevenless binding0.0121861478021528



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
lining cell7.56e-0957
barrier cell7.56e-0957
mesodermal cell8.91e-09119
mesothelial cell2.68e-0719
Uber Anatomy
Ontology termp-valuen
central nervous system6.46e-3682
neural tube3.66e-3557
neural rod3.66e-3557
future spinal cord3.66e-3557
neural keel3.66e-3557
regional part of nervous system2.82e-3094
nervous system2.82e-3094
anatomical conduit3.04e-30241
neural plate7.79e-3086
presumptive neural plate7.79e-3086
brain1.34e-2969
future brain1.34e-2969
adult organism1.57e-29115
regional part of brain5.94e-2959
neurectoderm5.26e-2790
tube1.87e-26194
anterior neural tube2.42e-2542
regional part of forebrain5.30e-2541
forebrain5.30e-2541
future forebrain5.30e-2541
anatomical cluster1.65e-24286
gray matter4.80e-2234
brain grey matter4.80e-2234
telencephalon5.92e-2234
epithelium2.45e-21309
regional part of telencephalon2.89e-2133
cell layer7.06e-21312
cerebral hemisphere2.37e-2032
ectoderm-derived structure3.90e-18169
pre-chordal neural plate3.29e-1761
anterior region of body5.20e-17129
craniocervical region5.20e-17129
head6.29e-17123
ectoderm7.88e-17173
presumptive ectoderm7.88e-17173
cerebral cortex2.71e-1525
pallium2.71e-1525
regional part of cerebral cortex1.25e-1322
neocortex2.11e-1220
organism subdivision1.43e-11365
posterior neural tube7.83e-1115
chordal neural plate7.83e-1115
multi-tissue structure1.29e-10347
multi-cellular organism5.78e-10659
segmental subdivision of nervous system3.11e-0913
anatomical system5.84e-09625
anatomical group8.02e-09626
segmental subdivision of hindbrain1.52e-0812
hindbrain1.52e-0812
presumptive hindbrain1.52e-0812
nucleus of brain2.44e-089
neural nucleus2.44e-089
embryo2.68e-08612
basal ganglion3.84e-089
nuclear complex of neuraxis3.84e-089
aggregate regional part of brain3.84e-089
collection of basal ganglia3.84e-089
cerebral subcortex3.84e-089
organ part4.74e-08219
compound organ3.02e-0769
epithelial tube3.47e-07118
brainstem4.22e-078
organ7.83e-07511
telencephalic nucleus8.46e-077


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.