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Coexpression cluster:C4036: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129711500660803!BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000284796446307061!BRCA1#672;3:20.1842306432238:0.000121570486027164:0.001642947721298!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190295092469869!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115353094924069!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00661064118182302!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325844186245929!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00437727667420197!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322787285742062!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462974607149359!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167673694939532!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00763252479670667!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00898642414343756!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582047225718244!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154316295530974!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391682800325774!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108837534450475!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000757391085483278!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128266928836777!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444784286143985!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156996745597674!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000858268728855296!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186827337756827!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00720923850805644!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294904239464988!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269915575445481!NR2C2#7182;3:32.6146109052409:2.88098172333076e-05:0.000605284349633759!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00471630482971657!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00485213278277747!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277206733321904!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203286025664777!SMARCC2#6601;3:94.1553744268976:1.19621075407887e-06:4.85735050331426e-05!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024690894242896!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064336645138926!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00543874769216502!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00629901430653449!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248470707361746!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616475615586848!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190586973028419!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00422105717083517!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140412078324439!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109576222395856
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|tfbs_overrepresentation_for_novel_motifs=1.66899,0.869629,0.690871,0.855819,0.641468,0.853988,2.1595,0.494933,0.491742,1.18351,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,1.46099,0.137917,0.596053,1.99037,0.567465,1.18324,0.598234,0.777097,0.718382,0.63803,0.461452,2.89234,0.939121,1.89324,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,2.14035,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,1.55552,2.26789,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,3.17067,4.24457,0.921547,1.7605,0.622396,0.703975,1.26794,0.684398,1.94007,1.58942,0.594137,1.66424,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,1.73097,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,4.20421,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,2.24188,0.936473,3.92523
}}
}}

Revision as of 16:30, 26 November 2012


Full id: C4036_salivary_CD19_lung_alveolar_bronchogenic_Eosinophils_renal



Phase1 CAGE Peaks

Hg19::chr20:42839224..42839236,-p@chr20:42839224..42839236
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Hg19::chr20:42839248..42839266,-p@chr20:42839248..42839266
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Hg19::chr20:42839289..42839310,-p@chr20:42839289..42839310
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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><br><br>disease_data<br>

Disease
Ontology termp-valuen
cell type cancer1.36e-15143
carcinoma4.09e-15106
disease of cellular proliferation7.80e-10239
cancer1.55e-09235
squamous cell carcinoma3.36e-0814


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
ATF3#467322.46317452600878.81932387510763e-050.00129711500660803
BHLHE40#8553344.87181354697741.10603738662898e-050.000284796446307061
BRCA1#672320.18423064322380.0001215704860271640.001642947721298
CCNT2#90536.336201576962630.003930750035764890.0190295092469869
CEBPB#105137.971147625824820.001974187055288560.0115353094924069
CHD2#1106310.34402283411690.0009033701102746880.00661064118182302
E2F1#186934.907389214879320.008460985347239390.0325844186245929
E2F4#1874312.66806031528440.0004917987006298980.00437727667420197
E2F6#187635.017155731697390.00791769806886330.0322787285742062
ELF1#199734.258097958807540.01295179875054610.0462974607149359
EP300#203336.77394172622320.003216880500103790.0167673694939532
ETS1#211339.728760922202340.001085840092584840.00763252479670667
FOS#235338.99795530889440.001372499272417130.00898642414343756
FOXA1#3169311.08141974938550.000734755275698670.00582047225718244
GABPB1#255337.067683836182170.002832212825417420.0154316295530974
HDAC2#3066313.41562023662630.0004140761399857210.00391682800325774
HMGN3#932438.178547723350590.001827766942164210.0108837534450475
HNF4G#3174328.75342252644684.20470658818262e-050.000757391085483278
IRF1#365937.63716375356390.002244692747297240.0128266928836777
JUN#3725312.51282919233630.0005103313992726250.00444784286143985
JUND#372736.994663941871030.002921845042734990.0156996745597674
MAFK#7975327.10073313782995.02195559325033e-050.000858268728855296
MAX#414936.452555509007120.003721913834265510.0186827337756827
MXI1#460139.96157162875930.001011470541259020.00720923850805644
MYC#460935.22228187160940.007020843755740150.0294904239464988
NFKB1#479035.488063424193840.006049381815655430.0269915575445481
NR2C2#7182332.61461090524092.88098172333076e-050.000605284349633759
NRF1#4899312.21027944771090.0005492172401020010.00471630482971657
RFX5#5993312.04791082719510.0005717246050312580.00485213278277747
SIN3A#2594235.408884726815140.006318961977991520.0277206733321904
SMARCB1#6598318.25271578115740.000164397760679890.00203286025664777
SMARCC2#6601394.15537442689761.19621075407887e-064.85735050331426e-05
SP1#666735.69838137814090.005403962701712170.024690894242896
STAT3#6774310.51946499715420.0008589184530415310.0064336645138926
TAF7#6879311.43306940492390.0006690181981945830.00543874769216502
TCF12#6938310.63446490218640.0008313523990202070.00629901430653449
TFAP2A#7020316.5186343730450.0002218033880766340.00248470707361746
TFAP2C#7022310.80922860986020.0007916746575753130.00616475615586848
USF1#739136.361499277207960.00388404057290560.0190586973028419
USF2#7392312.99219738506960.0004558979393427810.00422105717083517
ZBTB7A#5134137.35190930787590.002516255860282270.0140412078324439
ZNF263#1012738.221841637010680.001799043925565870.0109576222395856



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.

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