Coexpression cluster:C4788: Difference between revisions

Revision as of 16:57, 26 November 2012

Full id: C4788_mature_Adipocyte_heart_Hepatocyte_skeletal_mesodermal_Preadipocyte

Phase1 CAGE Peaks

Hg19::chr9:112542198..112542290,+	p2@PALM2 p6@PALM2-AKAP2
Hg19::chr9:112542293..112542312,+	p12@PALM2-AKAP2 p6@PALM2
Hg19::chr9:112542441..112542534,+	p1@PALM2 p3@PALM2-AKAP2

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:0022604	regulation of cell morphogenesis	0.00576945720004709
GO:0008360	regulation of cell shape	0.00576945720004709
GO:0022603	regulation of anatomical structure morphogenesis	0.00576945720004709
GO:0050793	regulation of developmental process	0.0243141410573413
GO:0032989	cellular structure morphogenesis	0.0328309588288394
GO:0000902	cell morphogenesis	0.0328309588288394

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
non-terminally differentiated cell	1.79e-15	106
fibroblast	5.17e-12	76
fat cell	9.41e-10	15
muscle precursor cell	8.35e-09	58
myoblast	8.35e-09	58
multi-potent skeletal muscle stem cell	8.35e-09	58
muscle cell	5.29e-08	55
contractile cell	9.17e-08	59
electrically responsive cell	1.23e-07	61
electrically active cell	1.23e-07	61

Uber Anatomy
Ontology term	p-value	n
multilaminar epithelium	5.05e-12	83
somite	1.26e-11	71
presomitic mesoderm	1.26e-11	71
presumptive segmental plate	1.26e-11	71
dermomyotome	1.26e-11	71
trunk paraxial mesoderm	1.26e-11	71
dense mesenchyme tissue	1.86e-11	73
paraxial mesoderm	1.86e-11	72
presumptive paraxial mesoderm	1.86e-11	72
organism subdivision	1.18e-10	264
trunk mesenchyme	1.41e-10	122
multi-cellular organism	3.81e-10	656
multi-tissue structure	4.84e-10	342
epithelial vesicle	1.29e-09	78
skeletal muscle tissue	1.89e-09	62
striated muscle tissue	1.89e-09	62
myotome	1.89e-09	62
cell layer	1.89e-09	309
integument	2.19e-09	46
integumental system	2.19e-09	46
muscle tissue	4.05e-09	64
musculature	4.05e-09	64
musculature of body	4.05e-09	64
trunk	5.02e-09	199
epithelium	6.91e-09	306
mesenchyme	9.83e-09	160
entire embryonic mesenchyme	9.83e-09	160
surface structure	1.22e-07	99
skin of body	2.14e-07	41
adipose tissue	3.78e-07	14
primary circulatory organ	4.15e-07	27
anatomical system	4.71e-07	624
anatomical group	4.79e-07	625

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	0.0281614408941662
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187566569647199
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00669226508255247
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191333103812881

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=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281614408941662!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187566569647199!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00669226508255247!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191333103812881
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+|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,1.18351,0.820209,0.985163,0.436625,2.13378,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,1.45286,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.78399,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,2.41357,1.45054,1.92922,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,1.48681,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,2.61709,0.921547,1.7605,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,1.86486,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,2.04753,1.08214,2.31409,0.773313,0.539692,0.853445,5.59159,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
 }}

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Coexpression cluster:C4788: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:57, 26 November 2012

Phase1 CAGE Peaks

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