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|full_id=C335_cerebellum_parietal_occipital_temporal_duodenum_brain_medial
|full_id=C335_cerebellum_parietal_occipital_temporal_duodenum_brain_medial
|id=C335
|id=C335
|ontology_enrichment_celltype=CL:0000133!5.18e-09!59;CL:0002319!7.54e-07!25
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.28e-38!82;UBERON:0000073!2.25e-38!94;UBERON:0001016!2.25e-38!94;UBERON:0005743!4.26e-37!86;UBERON:0007023!8.62e-36!115;UBERON:0001049!2.90e-35!57;UBERON:0005068!2.90e-35!57;UBERON:0006241!2.90e-35!57;UBERON:0007135!2.90e-35!57;UBERON:0002346!4.72e-35!90;UBERON:0003075!3.69e-33!86;UBERON:0007284!3.69e-33!86;UBERON:0000955!3.76e-32!69;UBERON:0006238!3.76e-32!69;UBERON:0002616!1.22e-30!59;UBERON:0000924!5.51e-29!173;UBERON:0006601!5.51e-29!173;UBERON:0004121!2.86e-27!169;UBERON:0003080!1.63e-26!42;UBERON:0002780!2.12e-26!41;UBERON:0001890!2.12e-26!41;UBERON:0006240!2.12e-26!41;UBERON:0003056!3.64e-24!61;UBERON:0002020!1.30e-22!34;UBERON:0003528!1.30e-22!34;UBERON:0001893!1.58e-22!34;UBERON:0000033!5.14e-22!123;UBERON:0002791!6.52e-22!33;UBERON:0000153!1.16e-21!129;UBERON:0007811!1.16e-21!129;UBERON:0001869!1.73e-21!32;UBERON:0000025!2.14e-19!194;UBERON:0004111!1.45e-18!241;UBERON:0000477!1.77e-17!286;UBERON:0000956!3.05e-17!25;UBERON:0000203!3.05e-17!25;UBERON:0002619!5.25e-16!22;UBERON:0000119!9.97e-15!312;UBERON:0001950!1.00e-14!20;UBERON:0000483!2.59e-14!309;UBERON:0000922!6.27e-12!612;UBERON:0000468!1.54e-11!659;UBERON:0000475!3.70e-11!365;UBERON:0000481!2.31e-10!347;UBERON:0000064!2.66e-10!219;UBERON:0002050!5.36e-10!605;UBERON:0005423!5.36e-10!605;UBERON:0003076!9.31e-10!15;UBERON:0003057!9.31e-10!15;UBERON:0000923!1.00e-09!604;UBERON:0005291!1.00e-09!604;UBERON:0006598!1.00e-09!604;UBERON:0002532!1.00e-09!604;UBERON:0000480!1.40e-09!626;UBERON:0000467!1.72e-09!625;UBERON:0004732!1.38e-08!13;UBERON:0004733!4.42e-08!12;UBERON:0002028!4.42e-08!12;UBERON:0007277!4.42e-08!12;UBERON:0002420!6.93e-07!9;UBERON:0007245!6.93e-07!9;UBERON:0010009!6.93e-07!9;UBERON:0010011!6.93e-07!9;UBERON:0000454!6.93e-07!9;UBERON:0002308!8.10e-07!9;UBERON:0000125!8.10e-07!9
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Revision as of 14:35, 21 May 2012


Full id: C335_cerebellum_parietal_occipital_temporal_duodenum_brain_medial



Phase1 CAGE Peaks

Hg19::chr10:13141961..13141973,-p6@CCDC3
Hg19::chr12:100378565..100378574,-p27@ANKS1B
Hg19::chr14:23982515..23982529,+p2@ENST00000554403
p2@uc001wkc.1
Hg19::chr17:48207157..48207212,-p2@SAMD14
Hg19::chr18:40695590..40695602,-p3@RIT2
Hg19::chr19:42547060..42547064,-p4@GRIK5
Hg19::chr1:151032142..151032195,+p5@MLLT11
Hg19::chr20:62795834..62795878,+p2@MYT1
Hg19::chr2:122247922..122247956,-p6@CLASP1
Hg19::chr2:131513104..131513119,+p1@FAM123C
Hg19::chr2:2336983..2336994,-p@chr2:2336983..2336994
-
Hg19::chr2:50809613..50809617,-p@chr2:50809613..50809617
-
Hg19::chr3:115371232..115371236,+p@chr3:115371232..115371236
+
Hg19::chr4:176733522..176733548,-p10@GPM6A
Hg19::chr5:87438363..87438394,+p@chr5:87438363..87438394
+
Hg19::chr8:10192316..10192321,-p@chr8:10192316..10192321
-
Hg19::chr8:10306862..10306874,+p@chr8:10306862..10306874
+
Hg19::chr8:85095305..85095312,+p17@RALYL
Hg19::chr8:85095736..85095748,+p7@RALYL
Hg19::chr8:85101923..85101927,+p@chr8:85101923..85101927
+
Hg19::chr8:85155756..85155760,+p@chr8:85155756..85155760
+
Hg19::chr8:85208884..85208887,+p@chr8:85208884..85208887
+
Hg19::chr8:85247963..85247966,+p@chr8:85247963..85247966
+
Hg19::chr8:85289710..85289715,+p@chr8:85289710..85289715
+
Hg19::chr8:9953136..9953190,+p3@MSRA
Hg19::chr8:9953214..9953226,+p5@MSRA
Hg19::chr9:73736417..73736430,-p8@TRPM3
Hg19::chr9:73736712..73736721,-p10@TRPM3
Hg19::chrX:10645578..10645591,-p15@MID1
Hg19::chrX:124338153..124338169,-p1@ENST00000422498
Hg19::chrX:124338174..124338186,-p2@ENST00000422498
Hg19::chrX:124338245..124338250,-p4@ENST00000422498
Hg19::chrX:23351515..23351543,-p@chrX:23351515..23351543
-
Hg19::chrX:32173579..32173593,-p5@DMD


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
neurectodermal cell5.18e-0959
neural cell7.54e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system1.28e-3882
regional part of nervous system2.25e-3894
nervous system2.25e-3894
adult organism8.62e-36115
neural tube2.90e-3557
neural rod2.90e-3557
future spinal cord2.90e-3557
neural keel2.90e-3557
neurectoderm4.72e-3590
neural plate3.69e-3386
presumptive neural plate3.69e-3386
brain3.76e-3269
future brain3.76e-3269
regional part of brain1.22e-3059
ectoderm5.51e-29173
presumptive ectoderm5.51e-29173
ectoderm-derived structure2.86e-27169
anterior neural tube1.63e-2642
regional part of forebrain2.12e-2641
forebrain2.12e-2641
future forebrain2.12e-2641
pre-chordal neural plate3.64e-2461
gray matter1.30e-2234
brain grey matter1.30e-2234
telencephalon1.58e-2234
head5.14e-22123
regional part of telencephalon6.52e-2233
anterior region of body1.16e-21129
craniocervical region1.16e-21129
cerebral hemisphere1.73e-2132
tube2.14e-19194
anatomical conduit1.45e-18241
anatomical cluster1.77e-17286
cerebral cortex3.05e-1725
pallium3.05e-1725
regional part of cerebral cortex5.25e-1622
cell layer9.97e-15312
neocortex1.00e-1420
epithelium2.59e-14309
embryo6.27e-12612
multi-cellular organism1.54e-11659
organism subdivision3.70e-11365
multi-tissue structure2.31e-10347
organ part2.66e-10219
embryonic structure5.36e-10605
developing anatomical structure5.36e-10605
posterior neural tube9.31e-1015
chordal neural plate9.31e-1015
germ layer1.00e-09604
embryonic tissue1.00e-09604
presumptive structure1.00e-09604
epiblast (generic)1.00e-09604
anatomical group1.40e-09626
anatomical system1.72e-09625
segmental subdivision of nervous system1.38e-0813
segmental subdivision of hindbrain4.42e-0812
hindbrain4.42e-0812
presumptive hindbrain4.42e-0812
basal ganglion6.93e-079
nuclear complex of neuraxis6.93e-079
aggregate regional part of brain6.93e-079
collection of basal ganglia6.93e-079
cerebral subcortex6.93e-079
nucleus of brain8.10e-079
neural nucleus8.10e-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.