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Coexpression cluster:C284: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;13:6.88372659347711:2.6472925649547e-08:1.82495437750035e-06!BCL11A#53335;13:8.0174547031933:4.37388609720519e-09:3.55213289351487e-07!BCLAF1#9774;13:6.11922649851269:1.04077750403072e-07:6.08951046181871e-06!EBF1#1879;15:2.90428266735946:9.4924302550943e-05:0.00137424441836955!EP300#2033;15:2.20889404115974:0.00183880453029562:0.0108824676341329!ETS1#2113;13:2.74943243453544:0.000548657796292662:0.00473642516010988!IRF4#3662;13:6.19323184625378:9.05832488493346e-08:5.34789368376238e-06!MEF2A#4205;13:5.29700003968201:5.41291926535482e-07:2.50918719553658e-05!NFKB1#4790;15:1.78958589919364:0.0137185725497341:0.0483108203298271!POU2F2#5452;14:2.77142906105207:0.000288319891135691:0.003063882896858!SPI1#6688;14:2.496968024333:0.00083681808146973:0.00631340342488023!SRF#6722;13:3.89920255235177:1.57387285244086e-05:0.000368303174627091!TCF12#6938;11:2.54302421574023:0.00301340716169468:0.01600311352386!ZBTB33#10009;15:10.3254538141243:6.165442395064e-12:7.92020465311302e-10
|tf_chipseq_enrich=BATF#10538;13:6.88372659347711:2.6472925649547e-08:1.82495437750035e-06!BCL11A#53335;13:8.0174547031933:4.37388609720519e-09:3.55213289351487e-07!BCLAF1#9774;13:6.11922649851269:1.04077750403072e-07:6.08951046181871e-06!EBF1#1879;15:2.90428266735946:9.4924302550943e-05:0.00137424441836955!EP300#2033;15:2.20889404115974:0.00183880453029562:0.0108824676341329!ETS1#2113;13:2.74943243453544:0.000548657796292662:0.00473642516010988!IRF4#3662;13:6.19323184625378:9.05832488493346e-08:5.34789368376238e-06!MEF2A#4205;13:5.29700003968201:5.41291926535482e-07:2.50918719553658e-05!NFKB1#4790;15:1.78958589919364:0.0137185725497341:0.0483108203298271!POU2F2#5452;14:2.77142906105207:0.000288319891135691:0.003063882896858!SPI1#6688;14:2.496968024333:0.00083681808146973:0.00631340342488023!SRF#6722;13:3.89920255235177:1.57387285244086e-05:0.000368303174627091!TCF12#6938;11:2.54302421574023:0.00301340716169468:0.01600311352386!ZBTB33#10009;15:10.3254538141243:6.165442395064e-12:7.92020465311302e-10
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|tfbs_overrepresentation_for_novel_motifs=0.0144922,0.00306992,0.0637571,0.174261,0.436409,0.692318,0.0719417,0.0296565,0.260627,0.0822716,0.145213,0.301982,0.00322103,0.879573,0.432473,0.144816,0.185123,0.696719,0.0168764,0.322802,4.73949,0.0787635,0.165427,0.241116,0.0925656,0.329864,0.313614,0.163422,0.123591,0.255066,0.126765,0.208225,0.0139693,0.0033945,0.00517222,0.278956,0.00493782,0.392362,0.448374,0.00555788,0.186888,0.0271609,0.0645901,2.53852,0.222081,0.0183191,0.917582,0.135901,0.395336,0.0440825,0.707115,0.562793,0.137253,0.259727,0.373267,0.0686071,0.128332,0.056637,0.00123731,0.0562884,0.235165,0.073311,0.00790399,0.168459,0.0806363,0.148683,0.444327,0.768402,0.201596,0.621219,0.7693,0.642019,3.03016e-05,0.3717,0.000356064,1.38427,0.990804,0.158618,0.578811,0.221988,1.1581,0.167826,0.0804887,1.12977,0.332069,1.34575e-08,1.15317e-05,0.146877,0.120022,0.860953,0.522821,0.311831,0.219125,1.77191,0.00831842,1.52774,0.447563,0.247685,0.122374,0.000651894,0.453017,0.61661,0.243872,1.04841,0.142306,0.035404,0.177726,0.869239,0.0923905,0.00670162,0.0702726,0.241987,0.0606813,0.0392115,0.482063,1.3924,8.50037e-07,1.25568,0.451255,0.016271,0.365229,1.24286,0.170099,0.603363,1.41302,0.159055,0.523637,0.222406,0.398874,0.00317161,0.312344,0.129111,0.410414,2.05098,0.533887,0.0345368,0.291051,1.96055,0.497634,1.29861,0.910351,2.04875,0.900289,1.27231,0.866781,0.438861,4.13594,1.14349,0.111271,0.0148394,1.904e-05,1.39715e-06,0.312627,0.00674439,0.542504,0.648552,0.111935,1.21648,0.230941,0.0159977,2.04536,0.298975,0.199042,0.0165227,0.463413,2.00519,0.0122665,0.0714183,2.74561e-07
}}
}}

Revision as of 14:02, 26 November 2012


Full id: C284_parietal_occipital_medial_temporal_olfactory_locus_hippocampus



Phase1 CAGE Peaks

Hg19::chr5:71411518..71411547,+p@chr5:71411518..71411547
+
Hg19::chr5:71479565..71479587,+p@chr5:71479565..71479587
+
Hg19::chr5:71482436..71482488,+p@chr5:71482436..71482488
+
Hg19::chr5:71489985..71489998,+p@chr5:71489985..71489998
+
Hg19::chr5:71490424..71490435,+p@chr5:71490424..71490435
+
Hg19::chr5:71490449..71490460,+p@chr5:71490449..71490460
+
Hg19::chr5:71490491..71490500,+p@chr5:71490491..71490500
+
Hg19::chr5:71490523..71490532,+p@chr5:71490523..71490532
+
Hg19::chr5:71490598..71490608,+p@chr5:71490598..71490608
+
Hg19::chr5:71490621..71490632,+p@chr5:71490621..71490632
+
Hg19::chr5:71490679..71490694,+p@chr5:71490679..71490694
+
Hg19::chr5:71490722..71490725,+p@chr5:71490722..71490725
+
Hg19::chr5:71490729..71490756,+p@chr5:71490729..71490756
+
Hg19::chr5:71490789..71490815,+p9@MAP1B
Hg19::chr5:71490821..71490833,+p19@MAP1B
Hg19::chr5:71490856..71490870,+p15@MAP1B
Hg19::chr5:71490880..71490891,+p23@MAP1B
Hg19::chr5:71490899..71490911,+p17@MAP1B
Hg19::chr5:71490923..71490924,+p56@MAP1B
Hg19::chr5:71490983..71491006,+p10@MAP1B
Hg19::chr5:71491080..71491109,+p14@MAP1B
Hg19::chr5:71491131..71491143,+p18@MAP1B
Hg19::chr5:71491157..71491183,+p6@MAP1B
Hg19::chr5:71491656..71491681,+p34@MAP1B
Hg19::chr5:71491821..71491840,+p@chr5:71491821..71491840
+
Hg19::chr5:71491859..71491877,+p@chr5:71491859..71491877
+
Hg19::chr5:71491884..71491904,+p@chr5:71491884..71491904
+
Hg19::chr5:71492510..71492528,+p@chr5:71492510..71492528
+
Hg19::chr5:71493786..71493803,+p36@MAP1B
Hg19::chr5:71493818..71493848,+p24@MAP1B
Hg19::chr5:71494196..71494211,+p33@MAP1B
Hg19::chr5:71494295..71494313,+p25@MAP1B
Hg19::chr5:71494567..71494578,+p@chr5:71494567..71494578
+
Hg19::chr5:71494879..71494901,+p@chr5:71494879..71494901
+
Hg19::chr5:71495032..71495074,+p@chr5:71495032..71495074
+
Hg19::chr5:71495080..71495197,+p@chr5:71495080..71495197
+
Hg19::chr5:71495203..71495271,+p@chr5:71495203..71495271
+
Hg19::chr5:71495849..71495883,+p@chr5:71495849..71495883
+
Hg19::chr5:71499530..71499550,+p@chr5:71499530..71499550
+
Hg19::chr5:71500942..71500967,+p@chr5:71500942..71500967
+
Hg19::chr5:71501161..71501215,+p@chr5:71501161..71501215
+
Hg19::chr5:71501221..71501269,+p@chr5:71501221..71501269
+
Hg19::chr5:71501410..71501437,+p@chr5:71501410..71501437
+
Hg19::chr5:71502973..71503023,+p29@MAP1B
Hg19::chr5:71503222..71503286,+p22@MAP1B
Hg19::chr5:71503803..71503818,+p4@MAP1B


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
fibroblast3.23e-0976
neural cell5.29e-0725
neurectodermal cell6.74e-0759
Uber Anatomy
Ontology termp-valuen
nervous system1.70e-3889
central nervous system8.39e-3781
neural tube2.81e-3256
neural rod2.81e-3256
future spinal cord2.81e-3256
neural keel2.81e-3256
brain3.94e-3068
future brain3.94e-3068
regional part of nervous system4.53e-3053
regional part of brain4.53e-3053
neural plate7.44e-2882
presumptive neural plate7.44e-2882
regional part of forebrain7.85e-2741
forebrain7.85e-2741
anterior neural tube7.85e-2741
future forebrain7.85e-2741
neurectoderm9.92e-2686
brain grey matter4.02e-2434
gray matter4.02e-2434
structure with developmental contribution from neural crest4.48e-24132
telencephalon1.44e-2334
cerebral hemisphere1.59e-2232
regional part of telencephalon1.63e-2232
pre-chordal neural plate7.98e-2261
ecto-epithelium2.94e-20104
ectoderm-derived structure6.11e-20171
ectoderm6.11e-20171
presumptive ectoderm6.11e-20171
cerebral cortex3.92e-1825
pallium3.92e-1825
regional part of cerebral cortex4.02e-1622
neocortex1.36e-1420
tube7.60e-14192
adult organism4.01e-13114
anatomical cluster8.72e-13373
organ system subdivision2.20e-12223
epithelium3.00e-12306
cell layer6.14e-12309
anatomical conduit2.48e-11240
multi-cellular organism7.60e-09656
multi-tissue structure3.62e-08342
neural nucleus1.99e-079
nucleus of brain1.99e-079
basal ganglion2.24e-079
nuclear complex of neuraxis2.24e-079
aggregate regional part of brain2.24e-079
collection of basal ganglia2.24e-079
cerebral subcortex2.24e-079
anatomical system3.92e-07624
anatomical group5.24e-07625
posterior neural tube7.01e-0715
chordal neural plate7.01e-0715
embryonic structure8.30e-07564


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
BATF#10538136.883726593477112.6472925649547e-081.82495437750035e-06
BCL11A#53335138.01745470319334.37388609720519e-093.55213289351487e-07
BCLAF1#9774136.119226498512691.04077750403072e-076.08951046181871e-06
EBF1#1879152.904282667359469.4924302550943e-050.00137424441836955
EP300#2033152.208894041159740.001838804530295620.0108824676341329
ETS1#2113132.749432434535440.0005486577962926620.00473642516010988
IRF4#3662136.193231846253789.05832488493346e-085.34789368376238e-06
MEF2A#4205135.297000039682015.41291926535482e-072.50918719553658e-05
NFKB1#4790151.789585899193640.01371857254973410.0483108203298271
POU2F2#5452142.771429061052070.0002883198911356910.003063882896858
SPI1#6688142.4969680243330.000836818081469730.00631340342488023
SRF#6722133.899202552351771.57387285244086e-050.000368303174627091
TCF12#6938112.543024215740230.003013407161694680.01600311352386
ZBTB33#100091510.32545381412436.165442395064e-127.92020465311302e-10



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

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