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Coexpression cluster:C2266: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.01e-59!115;UBERON:0001049!2.06e-28!57;UBERON:0005068!2.06e-28!57;UBERON:0006241!2.06e-28!57;UBERON:0007135!2.06e-28!57;UBERON:0002616!4.03e-24!59;UBERON:0003080!3.92e-23!42;UBERON:0002780!1.23e-22!41;UBERON:0001890!1.23e-22!41;UBERON:0006240!1.23e-22!41;UBERON:0000955!2.93e-20!69;UBERON:0006238!2.93e-20!69;UBERON:0001017!1.08e-19!82;UBERON:0005743!2.38e-19!86;UBERON:0001893!1.84e-18!34;UBERON:0003075!2.70e-18!86;UBERON:0007284!2.70e-18!86;UBERON:0002020!2.92e-18!34;UBERON:0003528!2.92e-18!34;UBERON:0002791!1.04e-17!33;UBERON:0000073!1.45e-17!94;UBERON:0001016!1.45e-17!94;UBERON:0001869!5.21e-17!32;UBERON:0002346!1.89e-16!90;UBERON:0002619!4.68e-15!22;UBERON:0000153!3.26e-14!129;UBERON:0007811!3.26e-14!129;UBERON:0000033!1.77e-13!123;UBERON:0001950!2.08e-13!20;UBERON:0003056!6.06e-13!61;UBERON:0000956!3.52e-12!25;UBERON:0000203!3.52e-12!25;UBERON:0004121!6.21e-11!169;UBERON:0000924!4.43e-10!173;UBERON:0006601!4.43e-10!173;UBERON:0002420!4.69e-08!9;UBERON:0007245!4.69e-08!9;UBERON:0010009!4.69e-08!9;UBERON:0010011!4.69e-08!9;UBERON:0000454!4.69e-08!9;UBERON:0000062!4.93e-08!511;UBERON:0002308!8.27e-08!9;UBERON:0000125!8.27e-08!9;UBERON:0002298!4.19e-07!8;UBERON:0004111!9.33e-07!241;UBERON:0000064!9.43e-07!219
|ontology_enrichment_uberon=UBERON:0007023!1.01e-59!115;UBERON:0001049!2.06e-28!57;UBERON:0005068!2.06e-28!57;UBERON:0006241!2.06e-28!57;UBERON:0007135!2.06e-28!57;UBERON:0002616!4.03e-24!59;UBERON:0003080!3.92e-23!42;UBERON:0002780!1.23e-22!41;UBERON:0001890!1.23e-22!41;UBERON:0006240!1.23e-22!41;UBERON:0000955!2.93e-20!69;UBERON:0006238!2.93e-20!69;UBERON:0001017!1.08e-19!82;UBERON:0005743!2.38e-19!86;UBERON:0001893!1.84e-18!34;UBERON:0003075!2.70e-18!86;UBERON:0007284!2.70e-18!86;UBERON:0002020!2.92e-18!34;UBERON:0003528!2.92e-18!34;UBERON:0002791!1.04e-17!33;UBERON:0000073!1.45e-17!94;UBERON:0001016!1.45e-17!94;UBERON:0001869!5.21e-17!32;UBERON:0002346!1.89e-16!90;UBERON:0002619!4.68e-15!22;UBERON:0000153!3.26e-14!129;UBERON:0007811!3.26e-14!129;UBERON:0000033!1.77e-13!123;UBERON:0001950!2.08e-13!20;UBERON:0003056!6.06e-13!61;UBERON:0000956!3.52e-12!25;UBERON:0000203!3.52e-12!25;UBERON:0004121!6.21e-11!169;UBERON:0000924!4.43e-10!173;UBERON:0006601!4.43e-10!173;UBERON:0002420!4.69e-08!9;UBERON:0007245!4.69e-08!9;UBERON:0010009!4.69e-08!9;UBERON:0010011!4.69e-08!9;UBERON:0000454!4.69e-08!9;UBERON:0000062!4.93e-08!511;UBERON:0002308!8.27e-08!9;UBERON:0000125!8.27e-08!9;UBERON:0002298!4.19e-07!8;UBERON:0004111!9.33e-07!241;UBERON:0000064!9.43e-07!219
|tf_chipseq_enrich=FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.0010692990143322!GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.7576989869892e-05!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249277514817408
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48988,0.00641248,0.224626,0.183585,0.0407862,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.357807,0.621787,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.000178798,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.0367692,0.064656,0.226143,0.12751,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,2.14704e-05,0.332403,0.0379537,0.6545,0.187953,0.051459,0.000276381,0.0726892,0.18732,0.00740893,2.35047e-05,0.003001,1.64608e-06,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.00265514,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.0757944,6.89614e-07,0.124464,0.186295,0.0159364,0.101893,0.142875,0.167635,0.0155918,0.787798,0.189107,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.00979133,0.535567,4.15088e-10,0.278645,0.365775,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.00233636,0.379174,0.0939463,0.0457255,0.0779623,0.0471607,0.163865,0.226359,0.960445,0.974549,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.0385301,0.0994829,0.0604041,0.144185,0.0925862,0.00516485,0.199201,0.049937,0.172796,0.0595495,6.36345e-05,0.149346,0.121978,0.22302,0.000482136,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.0988568,0.0271325,0.426452,0.196838,0.0826805,0.246601,0.0199582,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.00159724,0.220353,0.00318161,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.0114255,0.0316373,0.00231398,0.124417,0.0639386,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.00204396,0.119015,4.08996e-06,0.21618,0.243266,0.107021,0.238657,0.0016367,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.0487563,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.459091,0.0466753,0.0338476,0.296013,0.000760863,0.181196,3.91181e-06,0.523209,0.189126,0.25423,0.490559,0.45013,0.500698,0.472542,0.685908,0.399934,0.000134583,0.818701,0.029441,0.590496,0.603763,0.541914,0.259354,0.938109,0.934991,0.00523185,0.254935,0.722684,0.139104,0.00116273,0.608176,0.657141,0.824761,0.365494,0.00190736,0.56318,0.364079,0.680099,0.579886,0.421038,0.569409,0.328518,0.545608,0.0065017,0.324103,0.483764,0.829658,0.0698158,0.209437,0.55323,0.401218,0.598945,0.361291,0.464001,0.336867,0.579004,0.334776,0.113944,0.860705,0.261575,0.00026034,0.264245,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,8.35813e-07,0.126097,0.3955,0.442469,0.000111592,0.294954,0.0130252,0.00115593,0.667777,0.39549,0.0298727,0.357409,0.146291,0.721266,0.00575146,0.0171443,0.404625,0.172147,0.424691,0.132999,0.479581,0.62689,0.884725,0.274432,0.284496,0.512545,0.162017,0.563206,0.260945,0.0299859,0.263302,0.192292,0.0174164,0.775168,0.216102,0.254659,0.109605,1.53532e-05,0.0121932,7.52123e-06,0.417131,0.463987,0.260097,0.00578014,0.454761,0.639483,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.741477,0.385425,0.307816,0.461541,0.386339,0.0849889,0.598787,0.478745,5.90805e-05,0.000676019,0.00431644,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.00168296,0.000156291,0.559969,0.0105234,0.668972,0.574252,0.493455,0.0685505,0.125876,0.348802,6.22125e-12,0.579645,3.06683e-06,0.42505,0.254628,0.713293,0.139532,0.416962,0.632833,0.0828233,0.738545,0.0384092,0.22798,0.102495,0.350933,0.263896,0.0446972,1.14442e-05,4.00904e-06,0.242783,0.0947248,2.56773e-11,0.210656,0.000212417,0.02408,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.187728,0.231754,0.00317894,0.283107,0.000408231,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.00657048,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.000605968,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.0442657,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.0205476,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.000420752,0.000621734,0.223773,0.25788,0.181895,0.000242325,0.30702,9.21284e-05,0.170837,0.327002,0.28543,0.222656,0.00239762,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.0371525,0.139723,0.0708274,0.0710478,0.0206568,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.00297709,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.00173808,0.088258,0.117657,0.0486914,0.00104239,0.262778,0.000126367,0.0755696,0.0201006,0.00121144,0.00831677,0.325785,0.00352332,0.291176,0.376537,3.49391e-06,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.0109327,0.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}}
}}

Revision as of 12:24, 5 September 2012


Full id: C2266_rectal_extraskeletal_basal_heart_medulla_adipose_ductus



Phase1 CAGE Peaks

Hg19::chr13:49975564..49975588,-p7@CAB39L
Hg19::chr13:49975590..49975605,-p8@CAB39L
Hg19::chr13:49975606..49975627,-p5@CAB39L
Hg19::chr13:49975632..49975694,-p2@CAB39L


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.01e-59115
neural tube2.06e-2857
neural rod2.06e-2857
future spinal cord2.06e-2857
neural keel2.06e-2857
regional part of brain4.03e-2459
anterior neural tube3.92e-2342
regional part of forebrain1.23e-2241
forebrain1.23e-2241
future forebrain1.23e-2241
brain2.93e-2069
future brain2.93e-2069
central nervous system1.08e-1982
telencephalon1.84e-1834
neural plate2.70e-1886
presumptive neural plate2.70e-1886
gray matter2.92e-1834
brain grey matter2.92e-1834
regional part of telencephalon1.04e-1733
regional part of nervous system1.45e-1794
nervous system1.45e-1794
cerebral hemisphere5.21e-1732
neurectoderm1.89e-1690
regional part of cerebral cortex4.68e-1522
anterior region of body3.26e-14129
craniocervical region3.26e-14129
head1.77e-13123
neocortex2.08e-1320
pre-chordal neural plate6.06e-1361
cerebral cortex3.52e-1225
pallium3.52e-1225
ectoderm-derived structure6.21e-11169
ectoderm4.43e-10173
presumptive ectoderm4.43e-10173
basal ganglion4.69e-089
nuclear complex of neuraxis4.69e-089
aggregate regional part of brain4.69e-089
collection of basal ganglia4.69e-089
cerebral subcortex4.69e-089
organ4.93e-08511
nucleus of brain8.27e-089
neural nucleus8.27e-089
brainstem4.19e-078
anatomical conduit9.33e-07241
organ part9.43e-07219


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
FOXA1#3169411.08141974938556.62943068949433e-050.0010692990143322
GATA3#2625427.2365163572061.81561517799785e-066.7576989869892e-05
SPI1#668848.204323508522730.000220661881527680.00249277514817408



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:C2266&oldid=2131141"