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Difference between revisions of "Coexpression cluster:C522"

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|tf_chipseq_enrich=ATF3#467;4:5.28545282964912:0.00585762962104294:0.0262932470878112!CCNT2#905;8:2.98174191857065:0.00243014541697788:0.0136886876222292!E2F1#1869;11:3.17536949198074:9.04802704927931e-05:0.00132015492735357!ELF1#1997;11:2.755239855699:0.000348982991074966:0.00352353389451647!GABPB1#2553;11:4.57320718811788:2.44871881059722e-06:8.65454293942346e-05!HEY1#23462;9:2.13888231693832:0.0115734531098334:0.0422895482939574!MAX#4149;8:3.036496710121:0.00215601866543559:0.0124439034760667!MXI1#4601;10:5.85974801691723:1.03431706779201e-06:4.31746763561669e-05!NR2C2#7182;3:5.7555195715131:0.0141956977999394:0.0497979471492634!NRF1#4899;7:5.02776212552802:0.000229274601716291:0.0025282663001423!PAX5#5079;8:3.13861907349545:0.00173212486138333:0.0106619548769973!POLR2A#5430;15:1.89481162637477:0.00045412137082633:0.00422069785954713!RFX5#5993;6:4.25220382136298:0.00180848049643333:0.0109385472037412!SIN3A#25942;14:4.45437565737717:2.0970960182552e-08:1.48890966043885e-06!SP1#6667;8:2.68159123677219:0.00482897247791604:0.0226564715463196!SPI1#6688;6:2.89564359124332:0.0122532128785811:0.0444206081372532!SREBF1#6720;5:13.8252498354377:2.17206571175176e-05:0.000478179533873613!TAF1#6872;13:2.55644715968758:9.98053131212947e-05:0.00140460410956406!TBP#6908;11:2.3984986798859:0.00125412277486403:0.0084290706277125!USF1#7391;7:2.61944087885034:0.0107062462329532:0.0395231575526988!YY1#7528;11:3.1778163675525:8.98110145449078e-05:0.00131130610206286!ZEB1#6935;7:6.95406024251806:2.9174422587585e-05:0.000609999503628587!ZNF263#10127;6:2.90182646012142:0.0121295164888246:0.0439813412691857
 
|tf_chipseq_enrich=ATF3#467;4:5.28545282964912:0.00585762962104294:0.0262932470878112!CCNT2#905;8:2.98174191857065:0.00243014541697788:0.0136886876222292!E2F1#1869;11:3.17536949198074:9.04802704927931e-05:0.00132015492735357!ELF1#1997;11:2.755239855699:0.000348982991074966:0.00352353389451647!GABPB1#2553;11:4.57320718811788:2.44871881059722e-06:8.65454293942346e-05!HEY1#23462;9:2.13888231693832:0.0115734531098334:0.0422895482939574!MAX#4149;8:3.036496710121:0.00215601866543559:0.0124439034760667!MXI1#4601;10:5.85974801691723:1.03431706779201e-06:4.31746763561669e-05!NR2C2#7182;3:5.7555195715131:0.0141956977999394:0.0497979471492634!NRF1#4899;7:5.02776212552802:0.000229274601716291:0.0025282663001423!PAX5#5079;8:3.13861907349545:0.00173212486138333:0.0106619548769973!POLR2A#5430;15:1.89481162637477:0.00045412137082633:0.00422069785954713!RFX5#5993;6:4.25220382136298:0.00180848049643333:0.0109385472037412!SIN3A#25942;14:4.45437565737717:2.0970960182552e-08:1.48890966043885e-06!SP1#6667;8:2.68159123677219:0.00482897247791604:0.0226564715463196!SPI1#6688;6:2.89564359124332:0.0122532128785811:0.0444206081372532!SREBF1#6720;5:13.8252498354377:2.17206571175176e-05:0.000478179533873613!TAF1#6872;13:2.55644715968758:9.98053131212947e-05:0.00140460410956406!TBP#6908;11:2.3984986798859:0.00125412277486403:0.0084290706277125!USF1#7391;7:2.61944087885034:0.0107062462329532:0.0395231575526988!YY1#7528;11:3.1778163675525:8.98110145449078e-05:0.00131130610206286!ZEB1#6935;7:6.95406024251806:2.9174422587585e-05:0.000609999503628587!ZNF263#10127;6:2.90182646012142:0.0121295164888246:0.0439813412691857
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.871638,0.954273,0.431729,0.241986,0.364884,0.675949,0.300393,0.750341,0.740994,0.118722,1.82488,0.89216,1.78019,0.791753,0.362746,0.3998,1.22781,0.0827014,0.151825,0.461355,0.139663,0.456302,1.91484,0.356918,0.507569,0.934146,0.512008,0.658421,0.369737,0.741448,0.584851,0.522822,0.235149,0.13985,0.311809,1.14148,1.06147,0.677998,0.272549,0.37945,0.309718,0.190375,0.0808053,0.111922,0.161074,0.482397,0.301272,0.603923,0.0226973,0.369939,0.960528,1.51255,0.56057,1.44571,0.734926,0.293507,0.118135,0.267557,0.0979814,1.35239,0.559896,0.303183,0.0509632,1.17513,1.53741,0.4351,0.818746,1.17567,0.513487,1.01727,0.534356,0.200127,0.550473,0.73304,0.311418,1.64349,0.25554,1.1431,0.510572,0.165891,0.0404655,0.464358,0.317477,0.196319,0.684728,0.341004,0.455385,0.232513,1.786,1.27332,0.90828,0.659533,0.537982,0.0697368,0.366047,0.263897,0.624534,0.576706,1.01771,0.95583,0.274502,0.532876,0.571612,0.493139,0.425079,2.54694,2.09144,0.288402,0.507144,0.340143,0.882247,0.569087,0.422755,0.639318,0.862131,0.304665,0.268578,0.201199,1.93711,0.24923,0.725237,0.386689,0.23864,0.326716,0.968805,0.451097,0.295287,0.542501,0.765493,0.561324,0.660176,0.5898,0.779127,0.865701,0.920697,0.419578,0.19775,0.233646,0.879842,1.7239,1.32497,0.844052,0.296675,0.573485,0.426604,1.33087,0.412168,1.56567,0.188015,0.516702,0.294449,1.31098,1.58786,0.179266,0.818076,1.04704,0.374997,0.699176,0.170141,0.459614,0.842888,0.643319,0.509866,0.464924,0.440625,0.316832,0.223866,0.299321,1.72864
 
}}
 
}}

Revision as of 05:16, 26 November 2012


Full id: C522_pituitary_medulla_lung_testis_caudate_epididymis_thyroid



Phase1 CAGE Peaks

Hg19::chr10:119806476..119806520,+p1@CASC2
Hg19::chr10:75118471..75118533,-p1@TTC18
Hg19::chr11:101785727..101785767,+p1@KIAA1377
Hg19::chr11:102980126..102980199,+p2@DYNC2H1
Hg19::chr16:71598823..71598868,-p@chr16:71598823..71598868
-
Hg19::chr17:78388884..78388946,-p1@uc002jyi.1
Hg19::chr1:151693984..151694016,+p1@RIIAD1
Hg19::chr1:169396646..169396660,-p2@C1orf114
Hg19::chr1:42928945..42929017,+p1@CCDC30
Hg19::chr22:44208137..44208219,-p1@EFCAB6
Hg19::chr2:196933548..196933601,-p1@DNAH7
Hg19::chr3:119421849..119421962,+p1@C3orf15
Hg19::chr3:130745688..130745761,+p1@NEK11
Hg19::chr5:110074603..110074661,-p1@TMEM232
Hg19::chr6:163149104..163149130,+p3@PACRG
Hg19::chr9:34458771..34458850,+p1@DNAI1
Hg19::chrX:35937879..35937902,+p1@CXorf22


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:0030286dynein complex1.51318584945636e-05
GO:0005875microtubule associated complex0.00050209970312256
GO:0015630microtubule cytoskeleton0.00772417870359773
GO:0003777microtubule motor activity0.0147235821100474
GO:0044430cytoskeletal part0.0245198976747638
GO:0031573intra-S DNA damage checkpoint0.0245198976747638
GO:0042995cell projection0.0339156691283648
GO:0001539ciliary or flagellar motility0.0339156691283648
GO:0043232intracellular non-membrane-bound organelle0.0339156691283648
GO:0043228non-membrane-bound organelle0.0339156691283648
GO:0005858axonemal dynein complex0.0339156691283648
GO:0005856cytoskeleton0.0339156691283648
GO:0044447axoneme part0.0339156691283648
GO:0005930axoneme0.041969206624181
GO:0000077DNA damage checkpoint0.0489388637877478



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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism4.46e-34114
nervous system1.22e-3389
central nervous system2.44e-3381
neural tube1.79e-3156
neural rod1.79e-3156
future spinal cord1.79e-3156
neural keel1.79e-3156
regional part of nervous system1.02e-2953
regional part of brain1.02e-2953
neurectoderm3.65e-2986
brain1.84e-2868
future brain1.84e-2868
neural plate3.44e-2882
presumptive neural plate3.44e-2882
ectoderm-derived structure3.53e-26171
ectoderm3.53e-26171
presumptive ectoderm3.53e-26171
organ system subdivision3.60e-26223
regional part of forebrain7.84e-2641
forebrain7.84e-2641
anterior neural tube7.84e-2641
future forebrain7.84e-2641
pre-chordal neural plate4.41e-2261
brain grey matter2.95e-2134
gray matter2.95e-2134
telencephalon3.80e-2134
ecto-epithelium1.66e-20104
cerebral hemisphere4.21e-2032
regional part of telencephalon6.26e-2032
structure with developmental contribution from neural crest1.16e-19132
cerebral cortex8.51e-1625
pallium8.51e-1625
regional part of cerebral cortex6.94e-1522
anatomical cluster2.01e-14373
neocortex1.19e-1320
multi-tissue structure1.12e-12342
organ1.37e-09503
organ part2.61e-09218
posterior neural tube5.26e-0715
chordal neural plate5.26e-0715
neural nucleus6.35e-079
nucleus of brain6.35e-079
basal ganglion7.07e-079
nuclear complex of neuraxis7.07e-079
aggregate regional part of brain7.07e-079
collection of basal ganglia7.07e-079
cerebral subcortex7.07e-079
Disease
Ontology termp-valuen
cell type cancer1.15e-07143


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
ATF3#46745.285452829649120.005857629621042940.0262932470878112
CCNT2#90582.981741918570650.002430145416977880.0136886876222292
E2F1#1869113.175369491980749.04802704927931e-050.00132015492735357
ELF1#1997112.7552398556990.0003489829910749660.00352353389451647
GABPB1#2553114.573207188117882.44871881059722e-068.65454293942346e-05
HEY1#2346292.138882316938320.01157345310983340.0422895482939574
MAX#414983.0364967101210.002156018665435590.0124439034760667
MXI1#4601105.859748016917231.03431706779201e-064.31746763561669e-05
NR2C2#718235.75551957151310.01419569779993940.0497979471492634
NRF1#489975.027762125528020.0002292746017162910.0025282663001423
PAX5#507983.138619073495450.001732124861383330.0106619548769973
POLR2A#5430151.894811626374770.000454121370826330.00422069785954713
RFX5#599364.252203821362980.001808480496433330.0109385472037412
SIN3A#25942144.454375657377172.0970960182552e-081.48890966043885e-06
SP1#666782.681591236772190.004828972477916040.0226564715463196
SPI1#668862.895643591243320.01225321287858110.0444206081372532
SREBF1#6720513.82524983543772.17206571175176e-050.000478179533873613
TAF1#6872132.556447159687589.98053131212947e-050.00140460410956406
TBP#6908112.39849867988590.001254122774864030.0084290706277125
USF1#739172.619440878850340.01070624623295320.0395231575526988
YY1#7528113.17781636755258.98110145449078e-050.00131130610206286
ZEB1#693576.954060242518062.9174422587585e-050.000609999503628587
ZNF263#1012762.901826460121420.01212951648882460.0439813412691857



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.