Coexpression cluster:C3061: Difference between revisions

Revision as of 15:54, 26 November 2012

Full id: C3061_granulocyte_testicular_hepatoblastoma_HES3GFP_retinoblastoma_H9_Hodgkin

Phase1 CAGE Peaks

Hg19::chr10:96305516..96305531,+	p2@HELLS
Hg19::chr10:96305535..96305598,+	p1@HELLS
Hg19::chr10:96305610..96305620,+	p3@HELLS

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 cell_data disease_data

Cell Type
Ontology term	p-value	n
epithelial cell	5.81e-09	253

Disease
Ontology term	p-value	n
cancer	1.04e-53	235
disease of cellular proliferation	2.49e-51	239
cell type cancer	2.97e-34	143
carcinoma	8.01e-28	106
organ system cancer	4.19e-24	137
hematologic cancer	2.36e-14	51
immune system cancer	2.36e-14	51
leukemia	6.53e-11	39
germ cell and embryonal cancer	1.45e-07	22
germ cell cancer	1.45e-07	22
myeloid leukemia	2.09e-07	31

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
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00163912987221675
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0114903099569372
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00658296615594322
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171018632725133
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323517920729419
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00435316251335588
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320336433181225
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0459998949094839
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00759775247417042
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156137215727691
KAT2A#2648	3	616.09	4.23369446870294e-09	3.45980294692384e-07
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185684990416
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00718032707032021
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268538864897878
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172240077175227
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275356143872598
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0329685439778496
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245405887731158
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00540467138004672
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0327860600387919
ZBTB33#10009	3	31.6647250299812	3.14815888737575e-05	0.000633019957717821
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00241867639097049

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=BRCA1#672;3:20.1842306432238:0.000121570486027164:0.00163912987221675!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0114903099569372!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00658296615594322!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171018632725133!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323517920729419!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00435316251335588!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320336433181225!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0459998949094839!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00759775247417042!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156137215727691!KAT2A#2648;3:616.09:4.23369446870294e-09:3.45980294692384e-07!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185684990416!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00718032707032021!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268538864897878!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172240077175227!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275356143872598!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329685439778496!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245405887731158!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00540467138004672!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0327860600387919!ZBTB33#10009;3:31.6647250299812:3.14815888737575e-05:0.000633019957717821!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00241867639097049
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+|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,1.36391,1.45286,0.855276,0.567465,0.469078,0.598234,0.777097,1.32383,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,1.60305,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,2.20718,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,1.74644,0.459024,1.14559,0.960908,1.24629,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,2.50498,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,4.35547,0.714443,1.11698,0.960047,1.3017,0.936473,0.265282
 }}

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Coexpression cluster:C3061: Difference between revisions

From FANTOM5_SSTAR

Revision as of 15:54, 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