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Coexpression cluster:C2867: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!7.98e-44!115;UBERON:0001017!7.70e-24!82;UBERON:0005743!2.33e-23!86;UBERON:0001049!4.00e-23!57;UBERON:0005068!4.00e-23!57;UBERON:0006241!4.00e-23!57;UBERON:0007135!4.00e-23!57;UBERON:0000073!9.32e-23!94;UBERON:0001016!9.32e-23!94;UBERON:0002616!8.25e-22!59;UBERON:0000955!5.14e-21!69;UBERON:0006238!5.14e-21!69;UBERON:0003080!1.11e-19!42;UBERON:0002780!1.96e-19!41;UBERON:0001890!1.96e-19!41;UBERON:0006240!1.96e-19!41;UBERON:0002020!4.53e-18!34;UBERON:0003528!4.53e-18!34;UBERON:0001893!7.12e-18!34;UBERON:0001869!1.36e-17!32;UBERON:0002791!3.03e-17!33;UBERON:0002619!6.63e-15!22;UBERON:0002346!9.22e-15!90;UBERON:0003075!5.25e-14!86;UBERON:0007284!5.25e-14!86;UBERON:0001950!1.09e-13!20;UBERON:0000956!1.21e-13!25;UBERON:0000203!1.21e-13!25;UBERON:0000924!9.58e-13!173;UBERON:0006601!9.58e-13!173;UBERON:0004121!4.71e-12!169;UBERON:0000153!3.16e-11!129;UBERON:0007811!3.16e-11!129;UBERON:0000178!6.02e-11!15;UBERON:0000179!6.02e-11!15;UBERON:0000463!6.02e-11!15;UBERON:0003056!1.08e-10!61;UBERON:0000033!2.14e-10!123
|ontology_enrichment_uberon=UBERON:0007023!7.98e-44!115;UBERON:0001017!7.70e-24!82;UBERON:0005743!2.33e-23!86;UBERON:0001049!4.00e-23!57;UBERON:0005068!4.00e-23!57;UBERON:0006241!4.00e-23!57;UBERON:0007135!4.00e-23!57;UBERON:0000073!9.32e-23!94;UBERON:0001016!9.32e-23!94;UBERON:0002616!8.25e-22!59;UBERON:0000955!5.14e-21!69;UBERON:0006238!5.14e-21!69;UBERON:0003080!1.11e-19!42;UBERON:0002780!1.96e-19!41;UBERON:0001890!1.96e-19!41;UBERON:0006240!1.96e-19!41;UBERON:0002020!4.53e-18!34;UBERON:0003528!4.53e-18!34;UBERON:0001893!7.12e-18!34;UBERON:0001869!1.36e-17!32;UBERON:0002791!3.03e-17!33;UBERON:0002619!6.63e-15!22;UBERON:0002346!9.22e-15!90;UBERON:0003075!5.25e-14!86;UBERON:0007284!5.25e-14!86;UBERON:0001950!1.09e-13!20;UBERON:0000956!1.21e-13!25;UBERON:0000203!1.21e-13!25;UBERON:0000924!9.58e-13!173;UBERON:0006601!9.58e-13!173;UBERON:0004121!4.71e-12!169;UBERON:0000153!3.16e-11!129;UBERON:0007811!3.16e-11!129;UBERON:0000178!6.02e-11!15;UBERON:0000179!6.02e-11!15;UBERON:0000463!6.02e-11!15;UBERON:0003056!1.08e-10!61;UBERON:0000033!2.14e-10!123
|tf_chipseq_enrich=SRF#6722;3:10.3478836966259:0.00143989377840126:0.00924284365841729!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.0049979916345306!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279945762229799
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1,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,9.38741e-06,0.00237223,0.191914,0.184022,0.00201985,0.00118257,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.458838,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.833813,0.758305,0.278645,0.365775,0.155708,0.248017,0.22995,0.285695,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.012683,0.0939463,0.00500232,0.0779623,0.0471607,0.163865,0.226359,0.404165,0.499775,0.265324,0.279778,0.141699,0.00406251,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.0117528,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.0323312,0.107021,0.238657,0.20272,0.392453,0.0164195,0.0780061,0.315336,0.230477,0.279823,0.0487563,0.502112,0.140541,0.0478217,0.507599,0.0155059,0.0575231,0.174063,0.163504,0.459091,0.189333,0.0338476,0.296013,0.0895871,0.537932,0.459994,0.523209,0.548059,0.25423,0.490559,0.45013,0.153911,0.472542,0.322168,0.0510811,0.0074346,0.509113,0.483077,0.061678,0.0147688,0.541914,0.627201,0.938109,0.934991,0.290703,0.622694,0.722684,0.478691,0.360199,0.608176,0.290133,0.824761,0.365494,0.212703,0.201391,0.364079,0.680099,0.579886,0.421038,0.206595,0.328518,0.545608,0.310552,0.324103,0.483764,0.261345,0.19941,0.209437,0.11765,0.748403,0.0651244,0.361291,0.464001,0.336867,0.579004,0.334776,0.278028,0.586133,0.0376583,0.257956,0.264245,0.379063,0.326516,0.0391986,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.0215868,0.212239,0.294954,0.156999,0.35974,0.0999766,0.39549,0.234254,0.0103854,0.328421,0.721266,0.000785185,0.0171443,0.0158343,0.172147,0.424691,0.715362,0.139684,0.077723,0.635682,0.274432,0.284496,0.000881831,0.512178,0.563206,0.527709,0.684899,0.263302,0.552023,0.180735,0.775168,0.216102,0.254659,0.109605,0.0924199,0.0585759,0.226491,0.0175854,0.463987,0.0782409,0.503881,0.454761,0.000658711,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.187223,0.438176,0.349112,0.741477,0.385425,0.000569773,0.0250382,0.386339,0.0849889,0.598787,0.478745,0.611661,0.319747,0.136743,0.197104,0.608127,0.282281,0.0710918,0.2536,0.246827,0.564333,0.00168296,0.387134,0.559969,0.358813,0.0261538,0.574252,0.0317703,0.0685505,0.457747,0.348802,0.476541,0.215342,0.447581,0.0187686,0.254628,0.00183295,0.139532,0.416962,0.0806585,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.00849027,0.0239343,0.246234,0.211271,0.281295,0.0394002,0.118257,0.125087,0.215123,0.321224,0.469461,0.00757805,0.00394708,0.187728,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.036192,0.0432189,0.122439,0.16188,0.23235,0.0469743,0.0713545,0.112422,0.170886,0.267687,0.00686166,0.284866,0.0887542,0.0395756,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.113839,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,1.3342e-05,0.162089,0.330223,0.0136966,0.000167787,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.00699456,0.15156,2.82045e-05,0.313858,0.223773,0.036547,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.00239762,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.0371525,0.139723,0.0708274,0.0710478,0.196248,0.00545806,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.00571761,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.00173808,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.0755696,0.433518,0.184359,0.334474,0.325785,0.0364266,0.291176,0.0123861,0.322827,0.229571,0.359036,0.0641033,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.000371318,0.286696,0.150674,0.00325002,0.246177,0.35674,0.0737175,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0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}}
}}

Revision as of 13:13, 5 September 2012


Full id: C2867_neuroectodermal_CD19_smooth_carcinoid_cerebellum_umbilical_appendix



Phase1 CAGE Peaks

Hg19::chr6:70576369..70576372,+p9@COL19A1
Hg19::chr6:70576438..70576454,+p1@COL19A1
Hg19::chr6:70576457..70576468,+p2@COL19A1
Hg19::chr6:70917090..70917094,+p@chr6:70917090..70917094
+


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
lymphocyte of B lineage1.02e-1324
pro-B cell1.02e-1324
B cell3.73e-1114
Uber Anatomy
Ontology termp-valuen
adult organism7.98e-44115
central nervous system7.70e-2482
neural tube4.00e-2357
neural rod4.00e-2357
future spinal cord4.00e-2357
neural keel4.00e-2357
regional part of nervous system9.32e-2394
nervous system9.32e-2394
regional part of brain8.25e-2259
brain5.14e-2169
future brain5.14e-2169
anterior neural tube1.11e-1942
regional part of forebrain1.96e-1941
forebrain1.96e-1941
future forebrain1.96e-1941
gray matter4.53e-1834
brain grey matter4.53e-1834
telencephalon7.12e-1834
cerebral hemisphere1.36e-1732
regional part of telencephalon3.03e-1733
regional part of cerebral cortex6.63e-1522
neurectoderm9.22e-1590
neural plate5.25e-1486
presumptive neural plate5.25e-1486
neocortex1.09e-1320
cerebral cortex1.21e-1325
pallium1.21e-1325
ectoderm9.58e-13173
presumptive ectoderm9.58e-13173
ectoderm-derived structure4.71e-12169
anterior region of body3.16e-11129
craniocervical region3.16e-11129
blood6.02e-1115
haemolymphatic fluid6.02e-1115
organism substance6.02e-1115
pre-chordal neural plate1.08e-1061
head2.14e-10123


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
SRF#6722310.34788369662590.001439893778401260.00924284365841729
TRIM28#10155313.94289378394690.0005972858184258420.0049979916345306
ZNF263#1012736.166381227758010.006539814347975980.0279945762229799



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2867&oldid=2132020"