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Difference between revisions of "Coexpression cluster:C4626"

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|tf_chipseq_enrich=BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000285712190507406!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662596186157583!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327522923899309!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464756196429577!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168354270670645!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.0024403001550549!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583996242303602!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.0010768804714855!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393357267454691!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123363075420166!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000760144281397273!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295927799259725!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165948877279045!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278176559610292!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247808764260864!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00617178063666417!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249407020320151!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618736133821059!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.011008340083324
 
|tf_chipseq_enrich=BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000285712190507406!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662596186157583!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327522923899309!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464756196429577!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168354270670645!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.0024403001550549!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583996242303602!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.0010768804714855!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393357267454691!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123363075420166!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000760144281397273!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295927799259725!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165948877279045!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278176559610292!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247808764260864!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00617178063666417!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249407020320151!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618736133821059!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.011008340083324
 
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 +
|tfbs_overrepresentation_for_novel_motifs=1.66899,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.84557,1.91835,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,1.55576,1.78451,0.795576,1.21459,0.534793,0.439574,2.48753,0.137917,1.45286,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,2.41357,1.45054,0.430728,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,2.22068,1.48681,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,2.55998,0.703975,1.26794,0.684398,1.94007,1.58942,0.594137,2.36218,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,4.47109,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.42224
 
}}
 
}}

Revision as of 07:51, 26 November 2012


Full id: C4626_salivary_amniotic_choriocarcinoma_Keratinocyte_maxillary_cervical_esophagus



Phase1 CAGE Peaks

  Short description
Hg19::chr6:7541814..7541825,+ p7@DSP
Hg19::chr6:7541832..7541844,+ p3@DSP
Hg19::chr6:7541845..7541878,+ p2@DSP


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 cell4.25e-35253
endodermal cell5.51e-1958
endo-epithelial cell5.35e-1742
epithelial cell of alimentary canal1.39e-0920
respiratory epithelial cell6.92e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.35e-22160
endoderm5.35e-22160
presumptive endoderm5.35e-22160
digestive system1.58e-17145
digestive tract1.58e-17145
primitive gut1.58e-17145
subdivision of digestive tract2.05e-16118
foregut2.34e-1387
organ4.98e-12503
respiratory system7.36e-1274
subdivision of trunk8.75e-11112
immaterial anatomical entity1.24e-10117
multi-cellular organism1.67e-10656
organ part2.13e-10218
organism subdivision2.32e-10264
endo-epithelium1.10e-0982
respiratory tract5.83e-0954
trunk region element9.36e-09101
anatomical space1.15e-0895
primordium1.38e-08160
multi-tissue structure2.34e-08342
extraembryonic membrane1.36e-0714
membranous layer1.36e-0714
renal system4.19e-0748
respiratory primordium5.38e-0738
endoderm of foregut5.38e-0738
anatomical system5.72e-07624
urinary system structure7.20e-0747
anatomical group8.21e-07625
gland8.73e-0759
Disease
Ontology termp-valuen
carcinoma9.02e-22106
cell type cancer6.67e-15143
adenocarcinoma2.88e-0725


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285712190507406
CHD2#1106310.34402283411690.0009033701102746880.00662596186157583
E2F1#186934.907389214879320.008460985347239390.0327522923899309
ELF1#199734.258097958807540.01295179875054610.0464756196429577
EP300#203336.77394172622320.003216880500103790.0168354270670645
FOSL2#2355316.93020060456170.0002060162053171620.0024403001550549
FOXA1#3169311.08141974938550.000734755275698670.00583996242303602
FOXA2#3170324.63046375266526.68983856509345e-050.0010768804714855
HDAC2#3066313.41562023662630.0004140761399857210.00393357267454691
HNF4A#3172323.13229036295378.07584663437677e-050.00123363075420166
HNF4G#3174328.75342252644684.20470658818262e-050.000760144281397273
MYC#460935.22228187160940.007020843755740150.0295927799259725
RXRA#6256320.07461713913330.0001235730348432220.00165948877279045
SIN3A#2594235.408884726815140.006318961977991520.0278176559610292
SP1#666735.69838137814090.005403962701712170.0247808764260864
TCF7L2#6934310.77017656313730.0008003181298398380.00617178063666417
TFAP2A#7020316.5186343730450.0002218033880766340.00249407020320151
TFAP2C#7022310.80922860986020.0007916746575753130.00618736133821059
ZNF263#1012738.221841637010680.001799043925565870.011008340083324



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.