Coexpression cluster:C2674: Difference between revisions

Revision as of 15:39, 26 November 2012

Full id: C2674_tubular_rectal_hepatoblastoma_anaplastic_glioblastoma_chorionic_tridermal

Phase1 CAGE Peaks

Hg19::chr2:182756701..182756720,+	p7@SSFA2
Hg19::chr2:182756737..182756753,+	p10@SSFA2
Hg19::chr2:182756779..182756790,+	p18@SSFA2
Hg19::chr2:182756793..182756802,+	p17@SSFA2

Enriched pathways on this co-expression clusterSummary: 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. Analyst: Emmanuel Dimont link to source dataset data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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. Analyst: Erik Arner link to source dataset data

No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji links to source dataset uberon_data

Uber Anatomy
Ontology term	p-value	n
anatomical system	1.77e-13	624
anatomical group	2.69e-13	625
multi-cellular organism	1.94e-12	656
embryo	1.05e-10	592
anatomical cluster	5.84e-10	373
embryonic structure	6.16e-10	564
developing anatomical structure	6.55e-10	581
organ	1.53e-09	503
germ layer	2.77e-09	560
germ layer / neural crest	2.77e-09	560
embryonic tissue	2.77e-09	560
presumptive structure	2.77e-09	560
germ layer / neural crest derived structure	2.77e-09	560
epiblast (generic)	2.77e-09	560
anatomical conduit	3.55e-07	240

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon link to source data Novel motifs data Jaspar motifs data

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysisSummary: 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. Analyst: Erik Arner link to source dataset data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00818445891384525
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106617225829292
E2F4#1874	4	12.6680603152844	3.88145892637771e-05	0.000727914686320635
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00997923299069506
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0161098432175995
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.0039054989532757
HMGN3#9324	4	8.17854772335059	0.000223457028444047	0.00248351905860039
SPI1#6688	4	8.20432350852273	0.00022066188152768	0.00249628533848238
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322732711759564
TCF7L2#6934	4	10.7701765631373	7.42969445082454e-05	0.00115571918193277
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00249317052120137

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. Analyst:NA link to data source data

This analysis result is provided for C0 - C305 clusters.

@@ Line 8: / Line 8: @@
 |tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00818445891384525!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106617225829292!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.000727914686320635!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997923299069506!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161098432175995!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.0039054989532757!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248351905860039!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249628533848238!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322732711759564!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115571918193277!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249317052120137
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7,0.000705901,0.229571,0.359036,0.335984,0.171704,0.208256,0.003871,0.256405,0.0109327,0.302133,0.40806,0.151361,0.0433477,0.286696,0.150674,0.251128,0.000212201,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.0465068,0.00396262,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.045178,0.22741,0.203996,0.276721,0.00732664,0.264707,0.450113
+|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,1.42265,0.741427,0.534346,0.739643,0.821651,1.02453,0.392841,0.902371,1.68405,0.867962,0.341754,0.809319,0.532789,0.559384,2.39977,0.471262,0.356737,0.223552,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,4.53088,0.806311,0.682839,1.09415,1.93746,0.911389,0.49475,11.1906,0.491074,0.740899,1.17228,11.9877,0.493145,0.66492,3.08184,0.53106,0.648765,0.61613,0.822818,0.694903,0.99221,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,2.56328,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,3.8541,0.402607,1.28263,1.32819,6.51544,0.859396,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,2.2083,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,2.51889,1.15558,0.939507,0.749003,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,1.52945,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.85914,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,9.69978,1.24902,2.65458,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,8.1502
 }}

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Coexpression cluster:C2674: Difference between revisions

From FANTOM5_SSTAR

Revision as of 15:39, 26 November 2012

Phase1 CAGE Peaks

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	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0