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|full_id=C2398_brain_occipital_parietal_temporal_cerebellum_globus_optic
|full_id=C2398_brain_occipital_parietal_temporal_cerebellum_globus_optic
|id=C2398
|id=C2398
|ontology_enrichment_celltype=CL:0000066!4.40e-14!254;CL:0000221!2.38e-07!71
|ontology_enrichment_celltype=CL:0000066!4.54e-13!253;CL:0000221!7.34e-07!72
|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!1.34e-36!171;UBERON:0000924!1.34e-36!171;UBERON:0006601!1.34e-36!171;UBERON:0001017!1.37e-34!81;UBERON:0011216!8.15e-34!223;UBERON:0010371!8.84e-34!104;UBERON:0001049!9.82e-32!56;UBERON:0005068!9.82e-32!56;UBERON:0006241!9.82e-32!56;UBERON:0007135!9.82e-32!56;UBERON:0000955!3.10e-31!68;UBERON:0006238!3.10e-31!68;UBERON:0001016!7.13e-31!89;UBERON:0000073!8.32e-30!53;UBERON:0002616!8.32e-30!53;UBERON:0003075!4.64e-29!82;UBERON:0007284!4.64e-29!82;UBERON:0000477!6.33e-29!373;UBERON:0002346!2.93e-28!86;UBERON:0000481!8.39e-24!342;UBERON:0000064!1.89e-22!218;UBERON:0010314!2.22e-22!132;UBERON:0002780!2.81e-22!41;UBERON:0001890!2.81e-22!41;UBERON:0003080!2.81e-22!41;UBERON:0006240!2.81e-22!41;UBERON:0003056!7.49e-21!61;UBERON:0007023!2.13e-20!114;UBERON:0000119!1.21e-19!309;UBERON:0003528!1.34e-19!34;UBERON:0002020!1.34e-19!34;UBERON:0001893!1.53e-19!34;UBERON:0000483!1.58e-19!306;UBERON:0000062!1.70e-19!503;UBERON:0001869!2.09e-18!32;UBERON:0002791!2.25e-18!32;UBERON:0004111!5.12e-18!240;UBERON:0000025!1.14e-16!192;UBERON:0002619!4.77e-15!22;UBERON:0000956!1.11e-14!25;UBERON:0000203!1.11e-14!25;UBERON:0001950!7.40e-14!20;UBERON:0000468!9.86e-14!656;UBERON:0000467!6.84e-13!624;UBERON:0000480!8.51e-13!625;UBERON:0003076!1.41e-10!15;UBERON:0003057!1.41e-10!15;UBERON:0000922!2.04e-09!592;UBERON:0004732!2.13e-09!13;UBERON:0005423!5.98e-09!581;UBERON:0004733!9.06e-09!12;UBERON:0002028!9.06e-09!12;UBERON:0007277!9.06e-09!12;UBERON:0004119!9.08e-09!160;UBERON:0000925!9.08e-09!160;UBERON:0006595!9.08e-09!160;UBERON:0005177!1.78e-08!101;UBERON:0001007!1.06e-07!145;UBERON:0001555!1.06e-07!145;UBERON:0007026!1.06e-07!145;UBERON:0001048!1.29e-07!160;UBERON:0002050!2.68e-07!564;UBERON:0000063!2.82e-07!98;UBERON:0002680!4.48e-07!9;UBERON:0001895!4.48e-07!9;UBERON:0010092!4.48e-07!9;UBERON:0000923!5.44e-07!560;UBERON:0010316!5.44e-07!560;UBERON:0005291!5.44e-07!560;UBERON:0006598!5.44e-07!560;UBERON:0010317!5.44e-07!560;UBERON:0002532!5.44e-07!560
|tf_chipseq_enrich=BCLAF1#9774;4:21.6526476101218:4.54636978835329e-06:0.000141567774098339!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00511847690786296!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00816913023207687!CTCFL#140690;4:19.7464743589744:6.5732084880439e-06:0.000192782735546986!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106453335095488!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00996475197057434!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199509098048485!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160796703905151!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390149368677504!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185888461420264!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248035164137186!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.000793378676869637!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00443674694372509!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129319459220323!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.00024125017627599!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000437707485710988!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.00058387787794682!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321937405704633!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.000968355636344205!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243967892470455!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00119995186270156!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106763355110165!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00346298656096599!ZNF143#7702;4:13.5008765522279:3.00867915035614e-05:0.000620504426903722!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248665881236376!ZNF274#10782;4:1421.74615384615:2.33614176794641e-13:3.50049225398214e-11
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}}
}}

Revision as of 13:58, 19 October 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 cell4.54e-13253
ectodermal cell7.34e-0772
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure1.34e-36171
ectoderm1.34e-36171
presumptive ectoderm1.34e-36171
central nervous system1.37e-3481
organ system subdivision8.15e-34223
ecto-epithelium8.84e-34104
neural tube9.82e-3256
neural rod9.82e-3256
future spinal cord9.82e-3256
neural keel9.82e-3256
brain3.10e-3168
future brain3.10e-3168
nervous system7.13e-3189
regional part of nervous system8.32e-3053
regional part of brain8.32e-3053
neural plate4.64e-2982
presumptive neural plate4.64e-2982
anatomical cluster6.33e-29373
neurectoderm2.93e-2886
multi-tissue structure8.39e-24342
organ part1.89e-22218
structure with developmental contribution from neural crest2.22e-22132
regional part of forebrain2.81e-2241
forebrain2.81e-2241
anterior neural tube2.81e-2241
future forebrain2.81e-2241
pre-chordal neural plate7.49e-2161
adult organism2.13e-20114
cell layer1.21e-19309
brain grey matter1.34e-1934
gray matter1.34e-1934
telencephalon1.53e-1934
epithelium1.58e-19306
organ1.70e-19503
cerebral hemisphere2.09e-1832
regional part of telencephalon2.25e-1832
anatomical conduit5.12e-18240
tube1.14e-16192
regional part of cerebral cortex4.77e-1522
cerebral cortex1.11e-1425
pallium1.11e-1425
neocortex7.40e-1420
multi-cellular organism9.86e-14656
anatomical system6.84e-13624
anatomical group8.51e-13625
posterior neural tube1.41e-1015
chordal neural plate1.41e-1015
embryo2.04e-09592
segmental subdivision of nervous system2.13e-0913
developing anatomical structure5.98e-09581
segmental subdivision of hindbrain9.06e-0912
hindbrain9.06e-0912
presumptive hindbrain9.06e-0912
endoderm-derived structure9.08e-09160
endoderm9.08e-09160
presumptive endoderm9.08e-09160
trunk region element1.78e-08101
digestive system1.06e-07145
digestive tract1.06e-07145
primitive gut1.06e-07145
primordium1.29e-07160
embryonic structure2.68e-07564
organ segment2.82e-0798
regional part of metencephalon4.48e-079
metencephalon4.48e-079
future metencephalon4.48e-079
germ layer5.44e-07560
germ layer / neural crest5.44e-07560
embryonic tissue5.44e-07560
presumptive structure5.44e-07560
germ layer / neural crest derived structure5.44e-07560
epiblast (generic)5.44e-07560


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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