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Coexpression cluster:C3676: Difference between revisions

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|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.00896843217868814!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242873083498353!JUN#3725;3:12.5128291923363:0.000510331399272625:0.0044382130909013!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156593921290193!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308677117833396!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00202949618530107!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109008210127887!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00642398913758267!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613148658761318!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615191291387709
|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.00896843217868814!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242873083498353!JUN#3725;3:12.5128291923363:0.000510331399272625:0.0044382130909013!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156593921290193!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308677117833396!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00202949618530107!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109008210127887!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00642398913758267!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613148658761318!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615191291387709
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,1.99148,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,1.54465,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,1.32383,1.54087,0.461452,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.06461,1.02656,2.54768,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,1.34254,0.642354,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,2.36206,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,1.8537,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.42224
}}
}}

Revision as of 16:16, 26 November 2012


Full id: C3676_serous_endometrial_bile_signet_lung_small_Renal



Phase1 CAGE Peaks

Hg19::chr17:73085271..73085283,+p6@SLC16A5
Hg19::chr17:73085300..73085311,+p9@SLC16A5
Hg19::chr17:73085317..73085329,+p8@SLC16A5


Enriched pathways on this co-expression cluster<b>Summary:</b><br>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.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
renal cortex tubule8.86e-083
region of nephron tubule8.86e-083
proximal tubule8.86e-083
pulmonary alveolus epithelium3.51e-073
alveolus3.51e-073
pulmonary lobule3.51e-073
lobule3.51e-073
alveolus of lung3.51e-073
alveolar system3.51e-073
pulmonary acinus3.51e-073
alveolar sac3.51e-073
alveolar wall3.51e-073
Disease
Ontology termp-valuen
carcinoma4.19e-11106
adenocarcinoma1.18e-0825
cell type cancer7.73e-07143


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOS#235338.99795530889440.001372499272417130.00896843217868814
FOSL2#2355316.93020060456170.0002060162053171620.00242873083498353
JUN#3725312.51282919233630.0005103313992726250.0044382130909013
JUND#372736.994663941871030.002921845042734990.0156593921290193
NR3C1#2908314.9730233311730.0002978331194675480.00308677117833396
SMARCB1#6598318.25271578115740.000164397760679890.00202949618530107
SPI1#668838.204323508522730.001810593189410520.0109008210127887
STAT3#6774310.51946499715420.0008589184530415310.00642398913758267
TCF7L2#6934310.77017656313730.0008003181298398380.00613148658761318
TFAP2C#7022310.80922860986020.0007916746575753130.00615191291387709



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.