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|full_id=C1944_Astrocyte_Ciliary_Lens_colon_teratocarcinoma_gastric_Neural
|full_id=C1944_Astrocyte_Ciliary_Lens_colon_teratocarcinoma_gastric_Neural
|id=C1944
|id=C1944
|ontology_enrichment_celltype=CL:0002319!5.00e-12!25;CL:0000047!2.26e-10!8;CL:0000128!4.46e-10!7;CL:0000126!4.46e-10!7;CL:0000127!4.46e-10!7;CL:0002453!4.46e-10!7;CL:0000133!2.01e-09!59;CL:0000540!4.81e-08!6;CL:0000031!4.81e-08!6;CL:0000404!4.81e-08!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!6.38e-57!86;UBERON:0001017!2.06e-52!82;UBERON:0003075!3.31e-52!86;UBERON:0007284!3.31e-52!86;UBERON:0002346!3.76e-50!90;UBERON:0000073!4.00e-49!94;UBERON:0001016!4.00e-49!94;UBERON:0001049!2.22e-44!57;UBERON:0005068!2.22e-44!57;UBERON:0006241!2.22e-44!57;UBERON:0007135!2.22e-44!57;UBERON:0000955!7.05e-39!69;UBERON:0006238!7.05e-39!69;UBERON:0002616!8.73e-38!59;UBERON:0003056!1.46e-35!61;UBERON:0000033!3.65e-34!123;UBERON:0004121!5.80e-34!169;UBERON:0000153!1.89e-33!129;UBERON:0007811!1.89e-33!129;UBERON:0000924!2.35e-33!173;UBERON:0006601!2.35e-33!173;UBERON:0002780!9.27e-32!41;UBERON:0001890!9.27e-32!41;UBERON:0006240!9.27e-32!41;UBERON:0003080!1.08e-30!42;UBERON:0001893!7.97e-28!34;UBERON:0002020!1.06e-27!34;UBERON:0003528!1.06e-27!34;UBERON:0002791!7.88e-27!33;UBERON:0007023!2.05e-26!115;UBERON:0001869!3.23e-26!32;UBERON:0000956!1.38e-20!25;UBERON:0000203!1.38e-20!25;UBERON:0001950!5.08e-17!20;UBERON:0002619!5.87e-17!22;UBERON:0000025!4.80e-15!194;UBERON:0003076!1.32e-14!15;UBERON:0003057!1.32e-14!15;UBERON:0007625!6.86e-12!11;UBERON:0000475!1.53e-11!365;UBERON:0004733!2.45e-11!12;UBERON:0002028!2.45e-11!12;UBERON:0007277!2.45e-11!12;UBERON:0000483!6.45e-11!309;UBERON:0000119!1.44e-10!312;UBERON:0004111!3.11e-10!241;UBERON:0004732!3.31e-10!13;UBERON:0000477!1.10e-09!286;UBERON:0000064!8.17e-09!219;UBERON:0000062!1.39e-08!511;UBERON:0002420!1.40e-08!9;UBERON:0007245!1.40e-08!9;UBERON:0010009!1.40e-08!9;UBERON:0010011!1.40e-08!9;UBERON:0000454!1.40e-08!9;UBERON:0002308!1.57e-08!9;UBERON:0000125!1.57e-08!9;UBERON:0002680!2.76e-08!9;UBERON:0001895!2.76e-08!9;UBERON:0010092!2.76e-08!9;UBERON:0000481!5.01e-08!347;UBERON:0000020!5.37e-08!23;UBERON:0000468!1.40e-07!659;UBERON:0000970!1.66e-07!20;UBERON:0001032!1.72e-07!24;UBERON:0004456!1.72e-07!24;UBERON:0000200!4.06e-07!6;UBERON:0001871!4.28e-07!7;UBERON:0002104!5.58e-07!21;UBERON:0001456!6.08e-07!21;UBERON:0002298!6.08e-07!8;UBERON:0000019!6.95e-07!19;UBERON:0000047!6.95e-07!19;UBERON:0004088!6.95e-07!19;UBERON:0003072!6.95e-07!19;UBERON:0003071!6.95e-07!19;UBERON:0004128!6.95e-07!19;UBERON:0009663!8.47e-07!7
}}
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Revision as of 14:17, 21 May 2012


Full id: C1944_Astrocyte_Ciliary_Lens_colon_teratocarcinoma_gastric_Neural



Phase1 CAGE Peaks

Hg19::chr4:77356957..77356973,+p20@SHROOM3
Hg19::chr4:77356989..77357005,+p12@SHROOM3
Hg19::chr4:77357010..77357040,+p6@SHROOM3
Hg19::chr4:77357272..77357284,+p11@SHROOM3
Hg19::chr4:77357318..77357335,+p10@SHROOM3


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
neural cell5.00e-1225
neuronal stem cell2.26e-108
oligodendrocyte4.46e-107
macroglial cell4.46e-107
astrocyte4.46e-107
oligodendrocyte precursor cell4.46e-107
neurectodermal cell2.01e-0959
neuron4.81e-086
neuroblast4.81e-086
electrically signaling cell4.81e-086
Uber Anatomy
Ontology termp-valuen
central nervous system2.06e-5282
neural plate3.31e-5286
presumptive neural plate3.31e-5286
neurectoderm3.76e-5090
regional part of nervous system4.00e-4994
nervous system4.00e-4994
neural tube2.22e-4457
neural rod2.22e-4457
future spinal cord2.22e-4457
neural keel2.22e-4457
brain7.05e-3969
future brain7.05e-3969
regional part of brain8.73e-3859
pre-chordal neural plate1.46e-3561
head3.65e-34123
ectoderm-derived structure5.80e-34169
anterior region of body1.89e-33129
craniocervical region1.89e-33129
ectoderm2.35e-33173
presumptive ectoderm2.35e-33173
regional part of forebrain9.27e-3241
forebrain9.27e-3241
future forebrain9.27e-3241
anterior neural tube1.08e-3042
telencephalon7.97e-2834
gray matter1.06e-2734
brain grey matter1.06e-2734
regional part of telencephalon7.88e-2733
adult organism2.05e-26115
cerebral hemisphere3.23e-2632
cerebral cortex1.38e-2025
pallium1.38e-2025
neocortex5.08e-1720
regional part of cerebral cortex5.87e-1722
tube4.80e-15194
posterior neural tube1.32e-1415
chordal neural plate1.32e-1415
pigment epithelium of eye6.86e-1211
organism subdivision1.53e-11365
segmental subdivision of hindbrain2.45e-1112
hindbrain2.45e-1112
presumptive hindbrain2.45e-1112
epithelium6.45e-11309
cell layer1.44e-10312
anatomical conduit3.11e-10241
segmental subdivision of nervous system3.31e-1013
anatomical cluster1.10e-09286
organ part8.17e-09219
organ1.39e-08511
basal ganglion1.40e-089
nuclear complex of neuraxis1.40e-089
aggregate regional part of brain1.40e-089
collection of basal ganglia1.40e-089
cerebral subcortex1.40e-089
nucleus of brain1.57e-089
neural nucleus1.57e-089
regional part of metencephalon2.76e-089
metencephalon2.76e-089
future metencephalon2.76e-089
multi-tissue structure5.01e-08347
sense organ5.37e-0823
multi-cellular organism1.40e-07659
eye1.66e-0720
sensory system1.72e-0724
entire sense organ system1.72e-0724
gyrus4.06e-076
temporal lobe4.28e-077
visual system5.58e-0721
face6.08e-0721
brainstem6.08e-078
camera-type eye6.95e-0719
simple eye6.95e-0719
ocular region6.95e-0719
optic cup6.95e-0719
eye primordium6.95e-0719
optic vesicle6.95e-0719
telencephalic nucleus8.47e-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.