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Difference between revisions of "Coexpression cluster:C3745"

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325244524524397!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167414681358551!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000850925022134757!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444043164280877!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015670650357839!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294371472562426!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308891689812029!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246359273911614!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542691973601896!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.0062917111015414
 
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325244524524397!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167414681358551!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000850925022134757!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444043164280877!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015670650357839!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294371472562426!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308891689812029!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246359273911614!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542691973601896!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.0062917111015414
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,2.25583,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.85641,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,2.48753,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,1.82956,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,4.08293,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,3.76231,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,3.23473,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,4.35547,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408
 
}}
 
}}

Revision as of 07:19, 26 November 2012


Full id: C3745_Alveolar_Renal_Placental_Amniotic_amniotic_choriocarcinoma_pancreatic



Phase1 CAGE Peaks

  Short description
Hg19::chr19:10736157..10736169,+ p4@SLC44A2
Hg19::chr19:10736183..10736247,+ p2@SLC44A2
Hg19::chr19:10736263..10736275,+ p3@SLC44A2


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
disease_data


Cell Type
Ontology termp-valuen
epithelial cell3.55e-15253
endo-epithelial cell2.00e-0942
extraembryonic cell4.64e-0719
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.57e-15160
endoderm5.57e-15160
presumptive endoderm5.57e-15160
multi-tissue structure1.10e-13342
organism subdivision2.18e-13264
organ part2.21e-11218
renal system4.14e-1048
digestive system6.53e-10145
digestive tract6.53e-10145
primitive gut6.53e-10145
urinary system structure8.12e-1047
multi-cellular organism1.09e-09656
trunk5.46e-09199
organ system subdivision6.69e-09223
extraembryonic membrane1.08e-0814
membranous layer1.08e-0814
anatomical cluster2.44e-08373
subdivision of trunk3.88e-08112
respiratory system7.71e-0874
reproductive structure1.16e-0759
reproductive system1.16e-0759
organ1.50e-07503
endo-epithelium3.78e-0782
thoracic segment of trunk4.00e-0752
embryo4.72e-07592
subdivision of digestive tract9.19e-07118
Disease
Ontology termp-valuen
carcinoma1.76e-08106


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#promotersEnrichmentp-valueq-value
E2F1#186934.907389214879320.008460985347239390.0325244524524397
EP300#203336.77394172622320.003216880500103790.0167414681358551
GATA3#2625327.2365163572064.94721007899563e-050.000850925022134757
JUN#3725312.51282919233630.0005103313992726250.00444043164280877
JUND#372736.994663941871030.002921845042734990.015670650357839
MYC#460935.22228187160940.007020843755740150.0294371472562426
NR3C1#2908314.9730233311730.0002978331194675480.00308891689812029
SP1#666735.69838137814090.005403962701712170.0246359273911614
TAF7#6879311.43306940492390.0006690181981945830.00542691973601896
TCF12#6938310.63446490218640.0008313523990202070.0062917111015414



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.