Coexpression cluster:C3556: Difference between revisions

Revision as of 16:12, 26 November 2012

Full id: C3556_immature_Basophils_CD8_Natural_Peripheral_adult_CD4

Phase1 CAGE Peaks

Hg19::chr16:29819579..29819591,+	p32@MAZ
Hg19::chr16:29819630..29819645,+	p37@MAZ
Hg19::chr5:14664931..14664942,+	p6@FAM105B

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

GO ID	GO name	FDR corrected p-value
GO:0006369	transcription termination from RNA polymerase II promoter	0.00153067231837984
GO:0006353	transcription termination	0.00535735311432945
GO:0043624	cellular protein complex disassembly	0.00857176498292712
GO:0043241	protein complex disassembly	0.00857176498292712
GO:0032984	macromolecular complex disassembly	0.00857176498292712
GO:0022411	cellular component disassembly	0.0111520411767674
GO:0006367	transcription initiation from RNA polymerase II promoter	0.0111520411767674
GO:0006352	transcription initiation	0.0174113976215707
GO:0003702	RNA polymerase II transcription factor activity	0.0431649593783116
GO:0065004	protein-DNA complex assembly	0.0431649593783116

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

Cell Type
Ontology term	p-value	n
T cell	3.02e-16	25
pro-T cell	3.02e-16	25
hematopoietic stem cell	3.59e-16	168
angioblastic mesenchymal cell	3.59e-16	168
hematopoietic cell	3.91e-16	177
leukocyte	1.13e-14	136
hematopoietic oligopotent progenitor cell	7.84e-14	161
hematopoietic multipotent progenitor cell	7.84e-14	161
lymphoid lineage restricted progenitor cell	1.59e-12	52
lymphocyte	3.74e-12	53
common lymphoid progenitor	3.74e-12	53
nucleate cell	1.87e-11	55
CD4-positive, alpha-beta T cell	4.28e-11	6
mature alpha-beta T cell	5.80e-10	18
alpha-beta T cell	5.80e-10	18
immature T cell	5.80e-10	18
mature T cell	5.80e-10	18
immature alpha-beta T cell	5.80e-10	18
hematopoietic lineage restricted progenitor cell	1.18e-09	120
nongranular leukocyte	5.26e-09	115
circulating cell	2.07e-07	6
natural killer cell	8.83e-07	3
pro-NK cell	8.83e-07	3

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	0.0189740988623243
CTCFL#140690	2	13.1643162393162	0.00743336703699601	0.0306766278095715
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320050043583183
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461379667681385
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108577527827023
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127868149795449
SMC3#9126	2	10.0299552299552	0.012665637976747	0.045731601198046
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109238574733822

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 9: / Line 9: @@
 |tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189740988623243!CTCFL#140690;2:13.1643162393162:0.00743336703699601:0.0306766278095715!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320050043583183!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461379667681385!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108577527827023!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127868149795449!SMC3#9126;2:10.0299552299552:0.012665637976747:0.045731601198046!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109238574733822
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+|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,3.95039,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,1.26332,0.845342,0.635379,1.7611,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,0.439574,0.599922,1.36391,1.45286,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,1.10051,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,5.61317,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,1.50815,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,3.40309,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,1.76124,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408
 }}

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Coexpression cluster:C3556: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:12, 26 November 2012

Phase1 CAGE Peaks

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