Coexpression cluster:C3560: Difference between revisions

Revision as of 16:12, 26 November 2012

Full id: C3560_Macrophage_Mesenchymal_myxofibrosarcoma_renal_tenocyte_Hepatocyte_liver

Phase1 CAGE Peaks

Hg19::chr16:30996502..30996558,+	p1@HSD3B7
Hg19::chr16:30996559..30996574,+	p2@HSD3B7
Hg19::chr16:30996578..30996601,+	p3@HSD3B7

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
fibroblast	1.27e-12	76
skin fibroblast	5.13e-07	23

Uber Anatomy
Ontology term	p-value	n
trunk	4.47e-10	199
adipose tissue	3.13e-08	14
mesenchyme	8.24e-08	160
entire embryonic mesenchyme	8.24e-08	160
subdivision of trunk	1.13e-07	112
organism subdivision	3.57e-07	264

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	3	5.36025637307503	0.006492509252767	0.0279053118996557
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171516157206878
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320062217878272
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461395405296682
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167281309774119
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.0076120320465477
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00242681327172559
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127875124548615
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156505577196738
MEF2C#4208	3	41.3113544926241	1.41744912101957e-05	0.000340393121982439
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00719499876437481
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172696409437393
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00663232730642524
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.001651208314482
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276174284407205
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00308651772778556
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00154713227931158
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00642260931604528
YY1#7528	3	4.91117074985386	0.00844145534180826	0.032877760747459
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139948474700191
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00388602699450921
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109244926183019

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;3:5.36025637307503:0.006492509252767:0.0279053118996557!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171516157206878!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320062217878272!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461395405296682!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167281309774119!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.0076120320465477!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242681327172559!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127875124548615!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156505577196738!MEF2C#4208;3:41.3113544926241:1.41744912101957e-05:0.000340393121982439!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00719499876437481!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172696409437393!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663232730642524!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.001651208314482!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276174284407205!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308651772778556!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00154713227931158!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00642260931604528!YY1#7528;3:4.91117074985386:0.00844145534180826:0.032877760747459!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139948474700191!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388602699450921!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109244926183019
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954,0.0107847
+|tfbs_overrepresentation_for_novel_motifs=0.699513,4.27237,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,1.54465,0.667627,1.17594,0.575162,2.9777,2.2774,0.69094,1.26332,0.845342,1.53533,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,1.46099,1.36391,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,1.54087,0.461452,0.726632,0.939121,0.808003,1.28131,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,1.5923,1.45054,0.430728,2.79908,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.977977,0.303648,0.381882,1.053,2.0169,3.57435,1.36973,1.23218,0.543775,0.642354,1.37703,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,1.94007,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,3.30166,0.936473,1.42224
 }}

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Coexpression cluster:C3560: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:12, 26 November 2012

Phase1 CAGE Peaks

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