Coexpression cluster:C4703: Difference between revisions

Revision as of 16:54, 26 November 2012

Full id: C4703_amniotic_mesenchymal_cervical_seminal_chorionic_Fibroblast_glioblastoma

Phase1 CAGE Peaks

Hg19::chr7:86975001..86975019,+	p2@CROT
Hg19::chr7:86975021..86975036,+	p3@CROT
Hg19::chr7:86975045..86975051,+	p4@CROT

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 uberon_data

Cell Type
Ontology term	p-value	n
epithelial cell of alimentary canal	5.48e-08	20

Uber Anatomy
Ontology term	p-value	n
organ system subdivision	6.47e-11	223
orifice	6.88e-10	36
ectoderm-derived structure	3.11e-09	171
ectoderm	3.11e-09	171
presumptive ectoderm	3.11e-09	171
endoderm-derived structure	8.16e-09	160
endoderm	8.16e-09	160
presumptive endoderm	8.16e-09	160
extraembryonic membrane	2.20e-08	14
membranous layer	2.20e-08	14
organ component layer	6.06e-08	66
organ part	1.66e-07	218
digestive system	2.06e-07	145
digestive tract	2.06e-07	145
primitive gut	2.06e-07	145
reproductive structure	6.38e-07	59
reproductive system	6.38e-07	59
mucosa	8.66e-07	20

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.019115459256158
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00662875507250602
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.03243191232749
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00919359968391194
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322491113633126
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464963876566851
FOS#2353	3	8.9979553088944	0.00137249927241713	0.0090203543837375
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154825163713044
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109217388529974
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128745931042329
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270852862661939
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00200225137116847
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246682098030397
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00473499251601559
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00137360645088644
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247895840736205
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000942461143618049
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191206841100018
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140924091480062
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0110141478716322

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=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.019115459256158!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662875507250602!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.03243191232749!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00919359968391194!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322491113633126!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464963876566851!FOS#2353;3:8.9979553088944:0.00137249927241713:0.0090203543837375!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154825163713044!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109217388529974!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128745931042329!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270852862661939!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00200225137116847!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246682098030397!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00473499251601559!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00137360645088644!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247895840736205!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000942461143618049!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191206841100018!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140924091480062!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110141478716322
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+|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,1.49369,0.69094,2.74135,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,2.91665,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,0.63803,0.151453,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,1.5923,1.45054,0.430728,0.414196,0.396746,1.12884,2.69227,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.95969,0.303648,0.381882,3.90735,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,2.83477,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,0.188952,1.86486,1.10778,0.547323,1.44203,2.38853,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,5.23881,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.42224
 }}

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Coexpression cluster:C4703: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:54, 26 November 2012

Phase1 CAGE Peaks

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