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Coexpression cluster:C2398: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!4.89e-38!169;UBERON:0000924!1.02e-37!173;UBERON:0006601!1.02e-37!173;UBERON:0005743!4.31e-35!86;UBERON:0001017!5.08e-35!82;UBERON:0001049!5.07e-32!57;UBERON:0005068!5.07e-32!57;UBERON:0006241!5.07e-32!57;UBERON:0007135!5.07e-32!57;UBERON:0000955!1.56e-31!69;UBERON:0006238!1.56e-31!69;UBERON:0000073!1.59e-31!94;UBERON:0001016!1.59e-31!94;UBERON:0003075!1.53e-29!86;UBERON:0007284!1.53e-29!86;UBERON:0002616!2.22e-29!59;UBERON:0000033!6.76e-29!123;UBERON:0002346!8.28e-29!90;UBERON:0000153!7.07e-27!129;UBERON:0007811!7.07e-27!129;UBERON:0000475!3.25e-26!365;UBERON:0000481!1.05e-22!347;UBERON:0003080!1.48e-22!42;UBERON:0000064!2.50e-22!219;UBERON:0002780!2.77e-22!41;UBERON:0001890!2.77e-22!41;UBERON:0006240!2.77e-22!41;UBERON:0000119!2.98e-21!312;UBERON:0000483!4.45e-21!309;UBERON:0003056!5.94e-21!61;UBERON:0007023!1.12e-20!115;UBERON:0000062!1.81e-20!511;UBERON:0002020!1.11e-19!34;UBERON:0003528!1.11e-19!34;UBERON:0001893!1.30e-19!34;UBERON:0004111!2.86e-19!241;UBERON:0002791!4.52e-19!33;UBERON:0001869!1.86e-18!32;UBERON:0000477!2.32e-18!286;UBERON:0000025!7.55e-18!194;UBERON:0000468!6.96e-15!659;UBERON:0002619!7.04e-15!22;UBERON:0000956!1.21e-14!25;UBERON:0000203!1.21e-14!25;UBERON:0001950!1.05e-13!20;UBERON:0000467!1.65e-13!625;UBERON:0000480!2.23e-13!626;UBERON:0000922!5.15e-12!612;UBERON:0002050!3.15e-11!605;UBERON:0005423!3.15e-11!605;UBERON:0000923!6.07e-11!604;UBERON:0005291!6.07e-11!604;UBERON:0006598!6.07e-11!604;UBERON:0002532!6.07e-11!604;UBERON:0003076!1.41e-10!15;UBERON:0003057!1.41e-10!15;UBERON:0005177!3.28e-10!107;UBERON:0004732!2.12e-09!13;UBERON:0004119!4.52e-09!169;UBERON:0000925!4.52e-09!169;UBERON:0006595!4.52e-09!169;UBERON:0004733!9.16e-09!12;UBERON:0002028!9.16e-09!12;UBERON:0007277!9.16e-09!12;UBERON:0001007!3.78e-08!155;UBERON:0001555!3.78e-08!155;UBERON:0007026!3.78e-08!155;UBERON:0001048!6.37e-08!168;UBERON:0002680!4.42e-07!9;UBERON:0001895!4.42e-07!9;UBERON:0010092!4.42e-07!9;UBERON:0004921!7.54e-07!129;UBERON:0004185!7.54e-07!129
|ontology_enrichment_uberon=UBERON:0004121!4.89e-38!169;UBERON:0000924!1.02e-37!173;UBERON:0006601!1.02e-37!173;UBERON:0005743!4.31e-35!86;UBERON:0001017!5.08e-35!82;UBERON:0001049!5.07e-32!57;UBERON:0005068!5.07e-32!57;UBERON:0006241!5.07e-32!57;UBERON:0007135!5.07e-32!57;UBERON:0000955!1.56e-31!69;UBERON:0006238!1.56e-31!69;UBERON:0000073!1.59e-31!94;UBERON:0001016!1.59e-31!94;UBERON:0003075!1.53e-29!86;UBERON:0007284!1.53e-29!86;UBERON:0002616!2.22e-29!59;UBERON:0000033!6.76e-29!123;UBERON:0002346!8.28e-29!90;UBERON:0000153!7.07e-27!129;UBERON:0007811!7.07e-27!129;UBERON:0000475!3.25e-26!365;UBERON:0000481!1.05e-22!347;UBERON:0003080!1.48e-22!42;UBERON:0000064!2.50e-22!219;UBERON:0002780!2.77e-22!41;UBERON:0001890!2.77e-22!41;UBERON:0006240!2.77e-22!41;UBERON:0000119!2.98e-21!312;UBERON:0000483!4.45e-21!309;UBERON:0003056!5.94e-21!61;UBERON:0007023!1.12e-20!115;UBERON:0000062!1.81e-20!511;UBERON:0002020!1.11e-19!34;UBERON:0003528!1.11e-19!34;UBERON:0001893!1.30e-19!34;UBERON:0004111!2.86e-19!241;UBERON:0002791!4.52e-19!33;UBERON:0001869!1.86e-18!32;UBERON:0000477!2.32e-18!286;UBERON:0000025!7.55e-18!194;UBERON:0000468!6.96e-15!659;UBERON:0002619!7.04e-15!22;UBERON:0000956!1.21e-14!25;UBERON:0000203!1.21e-14!25;UBERON:0001950!1.05e-13!20;UBERON:0000467!1.65e-13!625;UBERON:0000480!2.23e-13!626;UBERON:0000922!5.15e-12!612;UBERON:0002050!3.15e-11!605;UBERON:0005423!3.15e-11!605;UBERON:0000923!6.07e-11!604;UBERON:0005291!6.07e-11!604;UBERON:0006598!6.07e-11!604;UBERON:0002532!6.07e-11!604;UBERON:0003076!1.41e-10!15;UBERON:0003057!1.41e-10!15;UBERON:0005177!3.28e-10!107;UBERON:0004732!2.12e-09!13;UBERON:0004119!4.52e-09!169;UBERON:0000925!4.52e-09!169;UBERON:0006595!4.52e-09!169;UBERON:0004733!9.16e-09!12;UBERON:0002028!9.16e-09!12;UBERON:0007277!9.16e-09!12;UBERON:0001007!3.78e-08!155;UBERON:0001555!3.78e-08!155;UBERON:0007026!3.78e-08!155;UBERON:0001048!6.37e-08!168;UBERON:0002680!4.42e-07!9;UBERON:0001895!4.42e-07!9;UBERON:0010092!4.42e-07!9;UBERON:0004921!7.54e-07!129;UBERON:0004185!7.54e-07!129
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}}
}}

Revision as of 12:45, 5 September 2012


Full id: C2398_brain_occipital_parietal_temporal_cerebellum_globus_optic



Phase1 CAGE Peaks

Hg19::chr17:27507377..27507391,-p4@MYO18A
Hg19::chr17:27507395..27507449,-p1@MYO18A
Hg19::chr17:27507450..27507461,-p5@MYO18A
Hg19::chr17:27507464..27507475,-p6@MYO18A


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
epithelial cell4.40e-14254
ectodermal cell2.38e-0771
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure4.89e-38169
ectoderm1.02e-37173
presumptive ectoderm1.02e-37173
central nervous system5.08e-3582
neural tube5.07e-3257
neural rod5.07e-3257
future spinal cord5.07e-3257
neural keel5.07e-3257
brain1.56e-3169
future brain1.56e-3169
regional part of nervous system1.59e-3194
nervous system1.59e-3194
neural plate1.53e-2986
presumptive neural plate1.53e-2986
regional part of brain2.22e-2959
head6.76e-29123
neurectoderm8.28e-2990
anterior region of body7.07e-27129
craniocervical region7.07e-27129
organism subdivision3.25e-26365
multi-tissue structure1.05e-22347
anterior neural tube1.48e-2242
organ part2.50e-22219
regional part of forebrain2.77e-2241
forebrain2.77e-2241
future forebrain2.77e-2241
cell layer2.98e-21312
epithelium4.45e-21309
pre-chordal neural plate5.94e-2161
adult organism1.12e-20115
organ1.81e-20511
gray matter1.11e-1934
brain grey matter1.11e-1934
telencephalon1.30e-1934
anatomical conduit2.86e-19241
regional part of telencephalon4.52e-1933
cerebral hemisphere1.86e-1832
anatomical cluster2.32e-18286
tube7.55e-18194
multi-cellular organism6.96e-15659
regional part of cerebral cortex7.04e-1522
cerebral cortex1.21e-1425
pallium1.21e-1425
neocortex1.05e-1320
anatomical system1.65e-13625
anatomical group2.23e-13626
embryo5.15e-12612
embryonic structure3.15e-11605
developing anatomical structure3.15e-11605
germ layer6.07e-11604
embryonic tissue6.07e-11604
presumptive structure6.07e-11604
epiblast (generic)6.07e-11604
posterior neural tube1.41e-1015
chordal neural plate1.41e-1015
trunk region element3.28e-10107
segmental subdivision of nervous system2.12e-0913
endoderm-derived structure4.52e-09169
endoderm4.52e-09169
presumptive endoderm4.52e-09169
segmental subdivision of hindbrain9.16e-0912
hindbrain9.16e-0912
presumptive hindbrain9.16e-0912
digestive system3.78e-08155
digestive tract3.78e-08155
primitive gut3.78e-08155
primordium6.37e-08168
regional part of metencephalon4.42e-079
metencephalon4.42e-079
future metencephalon4.42e-079
subdivision of digestive tract7.54e-07129
endodermal part of digestive tract7.54e-07129


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
BCLAF1#9774421.65264761012184.54636978835329e-060.000141567774098339
CCNT2#90546.336201576962630.0006203100587215640.00511847690786296
CTCF#1066445.360256373075030.001211145381643620.00816913023207687
CTCFL#140690419.74647435897446.5732084880439e-060.000192782735546986
E2F1#186944.907389214879320.001724022357361790.0106453335095488
E2F6#187645.017155731697390.00157802193473060.00996475197057434
EBF1#187948.9064668465690.00015887907472010.00199509098048485
ELF1#199744.258097958807540.003041525565781240.0160796703905151
GABPB1#255347.067683836182170.0004006876864423170.00390149368677504
HEY1#2346244.040111043105710.00375304636917980.0185888461420264
HMGN3#932448.178547723350590.0002234570284440470.00248035164137186
NRF1#4899412.21027944771094.49717228915276e-050.000793378676869637
PAX5#507946.669565531177830.0005052774169483260.00443674694372509
RAD21#5885410.35503389545638.6948481184721e-050.00129319459220323
SMARCB1#6598418.25271578115749.00423392720929e-060.00024125017627599
SMC3#9126415.04493284493281.95092670935632e-050.000437707485710988
SRF#6722413.79717826216782.75840773062708e-050.00058387787794682
TAF1#687243.343046285745290.008005664898701650.0321937405704633
TAF7#6879411.43306940492395.85061525419808e-050.000968355636344205
TBP#690843.706770687096390.005296377814784350.0243967892470455
TCF12#6938410.63446490218647.8163066689251e-050.00119995186270156
YY1#752844.911170749853860.00171871838055440.0106763355110165
ZBTB7A#5134147.35190930787590.000342223540015990.00346298656096599
ZNF143#7702413.50087655222793.00867915035614e-050.000620504426903722
ZNF263#1012748.221841637010680.0002187871180958320.00248665881236376
ZNF274#1078241421.746153846152.33614176794641e-133.50049225398214e-11



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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