Coexpression cluster:C3407: Difference between revisions

Revision as of 16:07, 26 November 2012

Full id: C3407_hepatocellular_rhabdomyosarcoma_myxofibrosarcoma_acute_Burkitt_retinoblastoma_teratocarcinoma

Phase1 CAGE Peaks

Hg19::chr14:21852119..21852143,-	p2@SUPT16H
Hg19::chr14:21852148..21852186,-	p1@SUPT16H
Hg19::chr14:21852189..21852206,-	p3@SUPT16H

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 disease_data

Disease
Ontology term	p-value	n
cancer	2.54e-50	235
disease of cellular proliferation	1.14e-49	239
cell type cancer	2.56e-30	143
organ system cancer	2.67e-23	137
carcinoma	7.14e-23	106
hematologic cancer	7.72e-16	51
immune system cancer	7.72e-16	51
leukemia	1.44e-12	39
myeloid leukemia	1.75e-10	31
germ cell and embryonal cancer	4.06e-07	22
germ cell cancer	4.06e-07	22

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
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.00129438078441873
BHLHE40#8553	3	44.8718135469774	1.10603738662898e-05	0.000284096012351559
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164061248096536
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.0065926260182362
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324313446867668
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00436277622484379
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460939449910817
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255363297774917
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00580286647298044
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107143083867474
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153818759892756
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00387274837363816
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108503468238895
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127798444087972
MAFF#23764	3	56.3153564899452	5.59409009993116e-06	0.000168904647570601
MAFK#7975	3	27.1007331378299	5.02195559325033e-05	0.000856726592949153
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186111729836663
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293746455013919
NFE2#4778	3	77.204260651629	2.17039522930409e-06	7.82443587688264e-05
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269053482431325
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000604190462254903
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275908721108515
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245876300690127
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189873297787721
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00420948854097964
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328532571061343
ZBTB33#10009	3	31.6647250299812	3.14815888737575e-05	0.000633385794719006

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.

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+|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,1.00813,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,1.99037,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,4.36839,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,1.02656,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,0.169933,0.303648,2.64731,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.250511,1.37083,2.09999,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
 }}

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Coexpression cluster:C3407: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:07, 26 November 2012

Phase1 CAGE Peaks

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