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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!6.76e-40!82;UBERON:0005743!4.07e-39!86;UBERON:0000073!8.56e-39!94;UBERON:0001016!8.56e-39!94;UBERON:0001049!9.44e-38!57;UBERON:0005068!9.44e-38!57;UBERON:0006241!9.44e-38!57;UBERON:0007135!9.44e-38!57;UBERON:0007023!7.84e-35!115;UBERON:0002616!7.51e-33!59;UBERON:0000955!6.42e-32!69;UBERON:0006238!6.42e-32!69;UBERON:0002780!6.73e-31!41;UBERON:0001890!6.73e-31!41;UBERON:0006240!6.73e-31!41;UBERON:0003080!1.07e-29!42;UBERON:0002346!7.31e-29!90;UBERON:0003075!9.56e-29!86;UBERON:0007284!9.56e-29!86;UBERON:0001893!3.12e-26!34;UBERON:0002020!3.94e-26!34;UBERON:0003528!3.94e-26!34;UBERON:0002791!2.45e-25!33;UBERON:0001869!3.68e-25!32;UBERON:0003056!1.60e-22!61;UBERON:0000924!2.08e-22!173;UBERON:0006601!2.08e-22!173;UBERON:0004121!5.59e-22!169;UBERON:0000033!1.51e-21!123;UBERON:0002619!7.13e-21!22;UBERON:0000153!1.02e-20!129;UBERON:0007811!1.02e-20!129;UBERON:0000956!9.35e-20!25;UBERON:0000203!9.35e-20!25;UBERON:0001950!2.87e-19!20;UBERON:0000025!1.82e-16!194;UBERON:0000481!4.59e-16!347;UBERON:0004111!7.69e-15!241;UBERON:0000062!9.50e-13!511;UBERON:0000064!1.72e-12!219;UBERON:0000477!1.82e-12!286;UBERON:0000922!2.13e-12!612;UBERON:0000475!2.42e-11!365;UBERON:0000468!4.29e-10!659;UBERON:0002050!4.72e-10!605;UBERON:0005423!4.72e-10!605;UBERON:0000923!9.72e-10!604;UBERON:0005291!9.72e-10!604;UBERON:0006598!9.72e-10!604;UBERON:0002532!9.72e-10!604;UBERON:0000119!3.43e-09!312;UBERON:0003076!3.98e-09!15;UBERON:0003057!3.98e-09!15;UBERON:0000483!4.48e-09!309;UBERON:0001871!3.49e-08!7;UBERON:0002420!4.76e-08!9;UBERON:0007245!4.76e-08!9;UBERON:0010009!4.76e-08!9;UBERON:0010011!4.76e-08!9;UBERON:0000454!4.76e-08!9;UBERON:0000489!7.24e-08!32;UBERON:0002308!8.44e-08!9;UBERON:0000125!8.44e-08!9;UBERON:0004732!9.59e-08!13;UBERON:0005177!2.21e-07!107;UBERON:0004733!3.28e-07!12;UBERON:0002028!3.28e-07!12;UBERON:0007277!3.28e-07!12;UBERON:0005409!3.60e-07!35;UBERON:0004921!3.95e-07!129;UBERON:0004185!3.95e-07!129;UBERON:0000467!4.45e-07!625;UBERON:0000480!5.68e-07!626
|ontology_enrichment_uberon=UBERON:0001017!6.76e-40!82;UBERON:0005743!4.07e-39!86;UBERON:0000073!8.56e-39!94;UBERON:0001016!8.56e-39!94;UBERON:0001049!9.44e-38!57;UBERON:0005068!9.44e-38!57;UBERON:0006241!9.44e-38!57;UBERON:0007135!9.44e-38!57;UBERON:0007023!7.84e-35!115;UBERON:0002616!7.51e-33!59;UBERON:0000955!6.42e-32!69;UBERON:0006238!6.42e-32!69;UBERON:0002780!6.73e-31!41;UBERON:0001890!6.73e-31!41;UBERON:0006240!6.73e-31!41;UBERON:0003080!1.07e-29!42;UBERON:0002346!7.31e-29!90;UBERON:0003075!9.56e-29!86;UBERON:0007284!9.56e-29!86;UBERON:0001893!3.12e-26!34;UBERON:0002020!3.94e-26!34;UBERON:0003528!3.94e-26!34;UBERON:0002791!2.45e-25!33;UBERON:0001869!3.68e-25!32;UBERON:0003056!1.60e-22!61;UBERON:0000924!2.08e-22!173;UBERON:0006601!2.08e-22!173;UBERON:0004121!5.59e-22!169;UBERON:0000033!1.51e-21!123;UBERON:0002619!7.13e-21!22;UBERON:0000153!1.02e-20!129;UBERON:0007811!1.02e-20!129;UBERON:0000956!9.35e-20!25;UBERON:0000203!9.35e-20!25;UBERON:0001950!2.87e-19!20;UBERON:0000025!1.82e-16!194;UBERON:0000481!4.59e-16!347;UBERON:0004111!7.69e-15!241;UBERON:0000062!9.50e-13!511;UBERON:0000064!1.72e-12!219;UBERON:0000477!1.82e-12!286;UBERON:0000922!2.13e-12!612;UBERON:0000475!2.42e-11!365;UBERON:0000468!4.29e-10!659;UBERON:0002050!4.72e-10!605;UBERON:0005423!4.72e-10!605;UBERON:0000923!9.72e-10!604;UBERON:0005291!9.72e-10!604;UBERON:0006598!9.72e-10!604;UBERON:0002532!9.72e-10!604;UBERON:0000119!3.43e-09!312;UBERON:0003076!3.98e-09!15;UBERON:0003057!3.98e-09!15;UBERON:0000483!4.48e-09!309;UBERON:0001871!3.49e-08!7;UBERON:0002420!4.76e-08!9;UBERON:0007245!4.76e-08!9;UBERON:0010009!4.76e-08!9;UBERON:0010011!4.76e-08!9;UBERON:0000454!4.76e-08!9;UBERON:0000489!7.24e-08!32;UBERON:0002308!8.44e-08!9;UBERON:0000125!8.44e-08!9;UBERON:0004732!9.59e-08!13;UBERON:0005177!2.21e-07!107;UBERON:0004733!3.28e-07!12;UBERON:0002028!3.28e-07!12;UBERON:0007277!3.28e-07!12;UBERON:0005409!3.60e-07!35;UBERON:0004921!3.95e-07!129;UBERON:0004185!3.95e-07!129;UBERON:0000467!4.45e-07!625;UBERON:0000480!5.68e-07!626
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}}
}}

Revision as of 14:15, 5 September 2012


Full id: C1635_brain_smallcell_occipital_somatostatinoma_temporal_duodenum_small



Phase1 CAGE Peaks

Hg19::chr11:45307817..45307898,-p1@SYT13
Hg19::chr7:158380402..158380413,-p7@PTPRN2
Hg19::chr7:158380420..158380433,-p4@PTPRN2
Hg19::chr7:158380440..158380454,-p6@PTPRN2
Hg19::chr7:158380468..158380523,-p2@PTPRN2


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:0019198transmembrane receptor protein phosphatase activity0.0203930061304151
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.0203930061304151
GO:0005887integral to plasma membrane0.0203930061304151
GO:0031226intrinsic to plasma membrane0.0203930061304151
GO:0030133transport vesicle0.0385377429525907
GO:0044459plasma membrane part0.0391926789972099



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
central nervous system6.76e-4082
regional part of nervous system8.56e-3994
nervous system8.56e-3994
neural tube9.44e-3857
neural rod9.44e-3857
future spinal cord9.44e-3857
neural keel9.44e-3857
adult organism7.84e-35115
regional part of brain7.51e-3359
brain6.42e-3269
future brain6.42e-3269
regional part of forebrain6.73e-3141
forebrain6.73e-3141
future forebrain6.73e-3141
anterior neural tube1.07e-2942
neurectoderm7.31e-2990
neural plate9.56e-2986
presumptive neural plate9.56e-2986
telencephalon3.12e-2634
gray matter3.94e-2634
brain grey matter3.94e-2634
regional part of telencephalon2.45e-2533
cerebral hemisphere3.68e-2532
pre-chordal neural plate1.60e-2261
ectoderm2.08e-22173
presumptive ectoderm2.08e-22173
ectoderm-derived structure5.59e-22169
head1.51e-21123
regional part of cerebral cortex7.13e-2122
anterior region of body1.02e-20129
craniocervical region1.02e-20129
cerebral cortex9.35e-2025
pallium9.35e-2025
neocortex2.87e-1920
tube1.82e-16194
multi-tissue structure4.59e-16347
anatomical conduit7.69e-15241
organ9.50e-13511
organ part1.72e-12219
anatomical cluster1.82e-12286
embryo2.13e-12612
organism subdivision2.42e-11365
multi-cellular organism4.29e-10659
embryonic structure4.72e-10605
developing anatomical structure4.72e-10605
germ layer9.72e-10604
embryonic tissue9.72e-10604
presumptive structure9.72e-10604
epiblast (generic)9.72e-10604
cell layer3.43e-09312
posterior neural tube3.98e-0915
chordal neural plate3.98e-0915
epithelium4.48e-09309
temporal lobe3.49e-087
basal ganglion4.76e-089
nuclear complex of neuraxis4.76e-089
aggregate regional part of brain4.76e-089
collection of basal ganglia4.76e-089
cerebral subcortex4.76e-089
cavitated compound organ7.24e-0832
nucleus of brain8.44e-089
neural nucleus8.44e-089
segmental subdivision of nervous system9.59e-0813
trunk region element2.21e-07107
segmental subdivision of hindbrain3.28e-0712
hindbrain3.28e-0712
presumptive hindbrain3.28e-0712
gastrointestinal system3.60e-0735
subdivision of digestive tract3.95e-07129
endodermal part of digestive tract3.95e-07129
anatomical system4.45e-07625
anatomical group5.68e-07626


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CHD2#110648.275218267293490.0004028373567101730.00387616829716729
E2F1#186943.925911371903460.007214984547106360.0298662612411907
E2F6#187644.013724585357910.006632118233933880.0282876662678192
EGR1#195843.990543275848110.0067800983001440.0287556014769031
ETS1#211347.783008737761870.0005121035947688870.00443920877606804
HMGN3#932446.542838178680470.00100801277768350.00721809026318048
IRF1#365946.109731002851120.001315525264767990.00880662413480575
REST#597847.720022972902420.0005286363773650570.00457114212747386
SIN3A#2594244.327107781452110.004977052855762880.0232364069379982
TAF1#687253.343046285745290.002394600090870310.0135147062356338
YY1#752843.928936599883080.007193866269917620.0298308663290688
ZBTB7A#5134145.881527446300720.001524947561042230.0097129961778185



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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