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Coexpression cluster:C2804: Difference between revisions

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|full_id=C2804_parietal_Mast_Neurons_occipital_Neural_Fibroblast_pineal
|full_id=C2804_parietal_Mast_Neurons_occipital_Neural_Fibroblast_pineal
|id=C2804
|id=C2804
|ontology_enrichment_celltype=CL:0000738!8.84e-18!140;CL:0000037!7.76e-15!172;CL:0000566!7.76e-15!172;CL:0002031!1.98e-14!124;CL:0002087!2.34e-13!119;CL:0002032!7.01e-13!165;CL:0000837!7.01e-13!165;CL:0000988!8.96e-13!182;CL:0000542!6.44e-12!53;CL:0000051!6.44e-12!53;CL:0000838!1.49e-11!52
|ontology_enrichment_celltype=CL:0000738!5.98e-17!136;CL:0002031!6.86e-14!120;CL:0000037!1.34e-13!168;CL:0000566!1.34e-13!168;CL:0002087!4.97e-13!115;CL:0000988!3.79e-12!177;CL:0002032!9.93e-12!161;CL:0000837!9.93e-12!161;CL:0000542!1.45e-11!53;CL:0000051!1.45e-11!53;CL:0002242!2.65e-11!55;CL:0000838!3.32e-11!52
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!3.85e-26!82;UBERON:0005743!7.17e-25!86;UBERON:0000073!6.31e-24!94;UBERON:0001016!6.31e-24!94;UBERON:0001049!6.29e-23!57;UBERON:0005068!6.29e-23!57;UBERON:0006241!6.29e-23!57;UBERON:0007135!6.29e-23!57;UBERON:0003080!1.45e-21!42;UBERON:0002780!1.79e-21!41;UBERON:0001890!1.79e-21!41;UBERON:0006240!1.79e-21!41;UBERON:0000955!1.20e-19!69;UBERON:0006238!1.20e-19!69;UBERON:0002616!3.36e-19!59;UBERON:0001893!4.23e-18!34;UBERON:0002020!4.48e-18!34;UBERON:0003528!4.48e-18!34;UBERON:0001869!1.59e-17!32;UBERON:0002791!1.59e-17!33;UBERON:0002346!2.35e-14!90;UBERON:0003075!4.35e-14!86;UBERON:0007284!4.35e-14!86;UBERON:0000956!9.92e-14!25;UBERON:0000203!9.92e-14!25;UBERON:0002619!1.07e-13!22;UBERON:0003056!3.15e-13!61;UBERON:0001950!9.38e-13!20;UBERON:0007023!3.32e-11!115
|ontology_enrichment_uberon=UBERON:0001017!2.32e-25!81;UBERON:0001016!2.61e-24!89;UBERON:0001049!6.83e-22!56;UBERON:0005068!6.83e-22!56;UBERON:0006241!6.83e-22!56;UBERON:0007135!6.83e-22!56;UBERON:0000073!8.01e-21!53;UBERON:0002616!8.01e-21!53;UBERON:0002780!1.14e-20!41;UBERON:0001890!1.14e-20!41;UBERON:0003080!1.14e-20!41;UBERON:0006240!1.14e-20!41;UBERON:0000955!4.85e-19!68;UBERON:0006238!4.85e-19!68;UBERON:0003528!6.62e-18!34;UBERON:0002020!6.62e-18!34;UBERON:0001893!9.71e-18!34;UBERON:0001869!4.35e-17!32;UBERON:0002791!5.43e-17!32;UBERON:0000956!1.96e-13!25;UBERON:0000203!1.96e-13!25;UBERON:0002346!2.31e-13!86;UBERON:0002619!2.81e-13!22;UBERON:0003075!3.80e-13!82;UBERON:0007284!3.80e-13!82;UBERON:0003056!1.58e-12!61;UBERON:0001950!2.18e-12!20;UBERON:0007023!3.74e-11!114;UBERON:0010371!7.39e-07!104
|tf_chipseq_enrich=BRCA1#672;4:20.1842306432238:6.02116732184487e-06:0.000179721261482182!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513226350493714!CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129281868983093!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106737311625175!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.000728176196895926!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101608545817134!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161204713811026!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435021399378639!ETS1#2113;4:9.72876092220234:0.000111595531741814:0.00154738791019427!FOSL2#2355;4:16.9302006045617:1.2165416097647e-05:0.000304249016240938!GTF2B#2959;4:31.9438299343242:9.59435337635006e-07:4.09491079800827e-05!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.000719045712742108!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186489870468536!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248484120460688!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392324148077657!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142646385284905!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088927241533373!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.000795259357783314!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444721626063258!POLR3A#11128;3:254.349082568807:1.01767661315947e-07:5.96772194282773e-06!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.0018863326553049!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157364990620097!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00797664306668982!STAT3#6774;3:7.88959874786568:0.00319076048168013:0.0167457202988036!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032306941126565!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.000971434668574234!TBP#6908;4:3.70677068709639:0.00529637781478435:0.024485343835964!TCF7L2#6934;3:8.07763242235301:0.00297838168583462:0.015867938830122!THAP1#55145;4:31.3691446028513:1.03171810326891e-06:4.3221663452588e-05!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508737960196975!ZBTB33#10009;4:31.6647250299812:9.93721537730495e-07:4.20345417898077e-05!ZNF143#7702;4:13.5008765522279:3.00867915035614e-05:0.000621732176066571!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249671195660081
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48,0.0273633,0.183585,0.271662,0.03989,0.171436,0.05892,0.0691994,4.38466e-08,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.357807,0.00325259,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.00269603,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.0262915,0.0367692,0.064656,3.6861e-10,0.0248217,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.00648069,0.159873,0.142462,0.143935,0.332403,0.0379537,0.000120758,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.0429523,0.245002,0.170848,0.00489168,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.00237223,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.0210393,0.0465855,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.0360207,0.0150607,0.278645,0.365775,0.155708,0.248017,0.22995,0.00463504,0.0760151,0.0629459,0.000627939,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.108863,0.0792764,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.00384141,0.0994829,0.0604041,0.144185,0.0925862,0.0466818,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.0501465,0.100006,0.00120288,8.2505e-05,0.251078,0.000372899,0.00928313,0.016612,0.223717,0.426452,0.0207859,0.0826805,0.246601,0.193021,0.000422824,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.00631475,0.0173373,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.000413166,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.32805,0.21618,0.243266,6.2488e-06,0.238657,0.20272,0.392453,0.0724243,0.0780061,4.74849e-05,0.00015932,0.279823,0.295555,0.502112,0.140541,0.0478217,0.158752,0.170854,0.0575231,0.00101058,0.00640224,0.459091,0.54832,0.0338476,0.296013,0.0895871,0.537932,0.459994,0.00100779,0.548059,0.25423,0.490559,0.45013,8.62945e-05,0.135135,0.685908,0.0133357,0.529642,0.244786,6.53506e-05,0.590496,0.0147688,0.541914,0.627201,0.000629457,0.00709718,0.290703,0.622694,0.138899,0.000570481,0.360199,0.241059,0.00485804,0.0021436,0.0768516,0.212703,0.201391,0.364079,0.00628541,0.579886,0.421038,0.0537414,0.328518,0.187186,0.310552,0.143396,0.483764,0.00961647,0.0698158,0.209437,0.0404917,0.00298496,0.00037168,0.0221843,0.464001,0.152018,0.0572388,0.870272,0.113944,0.0500888,0.261575,0.0365695,0.264245,0.379063,0.00074309,0.522925,0.436016,0.475063,0.202522,0.183837,0.000825542,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.025886,0.39549,0.234254,7.12346e-06,9.05517e-06,0.00995016,0.50338,0.620526,0.404625,0.0034658,0.00251166,0.357704,0.479581,0.62689,0.0682871,0.274432,0.284496,0.16228,0.512178,0.563206,0.103692,0.110875,0.00378836,0.552023,0.180735,0.0646927,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.0175854,0.000469228,0.627953,0.0342559,0.0237654,0.639483,0.483658,0.452129,0.301581,0.261657,0.000976975,0.466529,0.187223,0.438176,0.349112,0.0124698,0.385425,0.307816,0.461541,0.386339,0.382854,0.598787,0.478745,0.611661,0.319747,0.136743,2.35715e-05,0.608127,0.282281,6.01357e-05,0.2536,0.246827,0.564333,1.26985e-16,0.387134,0.00990479,0.358813,0.303004,0.0113028,0.493455,0.346636,0.00360135,0.348802,0.476541,0.000281674,0.447581,0.42505,0.254628,6.6811e-06,0.139532,0.0175608,0.264955,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.0331645,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.0191872,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.00317461,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.0016375,0.233244,0.207281,0.327401,0.0205476,0.27845,0.161712,0.237871,0.239139,0.095257,0.0612213,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,2.18871e-09,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.0371525,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.111581,0.184359,0.334474,0.325785,0.257476,0.0472356,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696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}}
}}

Revision as of 14:26, 19 October 2012


Full id: C2804_parietal_Mast_Neurons_occipital_Neural_Fibroblast_pineal



Phase1 CAGE Peaks

Hg19::chr5:138629349..138629386,+p3@MATR3
Hg19::chr5:138629389..138629416,+p4@MATR3
Hg19::chr5:138629417..138629446,+p1@MATR3
Hg19::chr5:138629628..138629688,+p2@MATR3


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>


Uber Anatomy
Ontology termp-valuen
central nervous system2.32e-2581
nervous system2.61e-2489
neural tube6.83e-2256
neural rod6.83e-2256
future spinal cord6.83e-2256
neural keel6.83e-2256
regional part of nervous system8.01e-2153
regional part of brain8.01e-2153
regional part of forebrain1.14e-2041
forebrain1.14e-2041
anterior neural tube1.14e-2041
future forebrain1.14e-2041
brain4.85e-1968
future brain4.85e-1968
brain grey matter6.62e-1834
gray matter6.62e-1834
telencephalon9.71e-1834
cerebral hemisphere4.35e-1732
regional part of telencephalon5.43e-1732
cerebral cortex1.96e-1325
pallium1.96e-1325
neurectoderm2.31e-1386
regional part of cerebral cortex2.81e-1322
neural plate3.80e-1382
presumptive neural plate3.80e-1382
pre-chordal neural plate1.58e-1261
neocortex2.18e-1220
adult organism3.74e-11114
ecto-epithelium7.39e-07104


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
BRCA1#672420.18423064322386.02116732184487e-060.000179721261482182
CCNT2#90546.336201576962630.0006203100587215640.00513226350493714
CHD2#1106410.34402283411698.73193255208051e-050.00129281868983093
E2F1#186944.907389214879320.001724022357361790.0106737311625175
E2F4#1874412.66806031528443.88145892637771e-050.000728176196895926
EGR1#195844.988179094810140.001615011500076050.0101608545817134
ELF1#199744.258097958807540.003041525565781240.0161204713811026
EP300#203346.77394172622320.0004748459821442640.00435021399378639
ETS1#211349.728760922202340.0001115955317418140.00154738791019427
FOSL2#2355416.93020060456171.2165416097647e-050.000304249016240938
GTF2B#2959431.94382993432429.59435337635006e-074.09491079800827e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.000719045712742108
HEY1#2346244.040111043105710.00375304636917980.0186489870468536
HMGN3#932448.178547723350590.0002234570284440470.00248484120460688
JUND#372746.994663941871030.000417684217818580.00392324148077657
MXI1#460149.96157162875930.0001015224754950450.00142646385284905
MYC#460945.22228187160940.001344309395272740.0088927241533373
NRF1#4899412.21027944771094.49717228915276e-050.000795259357783314
PAX5#507946.669565531177830.0005052774169483260.00444721626063258
POLR3A#111283254.3490825688071.01767661315947e-075.96772194282773e-06
POU2F2#545249.106124057742520.000145395665174930.0018863326553049
REST#597849.650028716128020.0001152825614219170.00157364990620097
SIN3A#2594245.408884726815140.001168172384885160.00797664306668982
STAT3#677437.889598747865680.003190760481680130.0167457202988036
TAF1#687243.343046285745290.008005664898701650.032306941126565
TAF7#6879411.43306940492395.85061525419808e-050.000971434668574234
TBP#690843.706770687096390.005296377814784350.024485343835964
TCF7L2#693438.077632422353010.002978381685834620.015867938830122
THAP1#55145431.36914460285131.03171810326891e-064.3221663452588e-05
USF1#739146.361499277207960.0006105011399140830.00508737960196975
ZBTB33#10009431.66472502998129.93721537730495e-074.20345417898077e-05
ZNF143#7702413.50087655222793.00867915035614e-050.000621732176066571
ZNF263#1012748.221841637010680.0002187871180958320.00249671195660081



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.