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Coexpression cluster:C2464: Difference between revisions

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|tf_chipseq_enrich=BCL3#602;4:34.5471028037383:7.01262157705428e-07:3.14871532625096e-05!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199629110739804!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.016088628877868!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434259540535594!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391654893380811!MAFK#7975;4:27.1007331378299:1.85228494563408e-06:6.84781548449834e-05!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.0076792942298207!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.0044374931171095!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188375857526417!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322185517458095!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244183288128841!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106852329868874!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248828354860183
|tf_chipseq_enrich=BCL3#602;4:34.5471028037383:7.01262157705428e-07:3.14871532625096e-05!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199629110739804!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.016088628877868!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434259540535594!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391654893380811!MAFK#7975;4:27.1007331378299:1.85228494563408e-06:6.84781548449834e-05!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.0076792942298207!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.0044374931171095!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188375857526417!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322185517458095!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244183288128841!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106852329868874!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248828354860183
|tfbs_overrepresentation=0.191353,0.0774498,6.63941e-05,0.0631091,0.257053,0.0110447,0.0569281,0.160638,0.043387,0.0341265,0.0175562,0.00510754,0.00020201,0.0143109,0.193153,0.0816702,0.0179544,0.128744,0.0698403,0.141416,0.243245,0.0158619,0.00602909,0.124486,0.0550418,0.276459,0.268949,0.119094,6.47665e-05,0.122514,0.26347,0.0117122,0.0239693,0.267529,0.0877018,0.111013,0.460009,0.0568767,0.157159,0.0879352,0.126525,0.0326801,0.182216,0.2375,0.157881,0.0480278,0.0503649,0.234372,7.04141e-07,0.158244,0.19996,6.45863e-05,0.0924421,0.12203,0.000251123,0.0508907,0.140644,0.273035,0.103044,0.138225,0.0390464,0.194086,0.142115,0.0999599,0.0720888,0.0667453,3.1959e-05,0.0792005,0.113084,0.216289,0.470097,0.0892037,0.116917,0.155921,0.00995563,0.0227583,1.25323e-05,5.00306e-07,0.0493551,0.00965832,0.125428,2.98237e-05,0.0562614,0.150119,0.0114792,0.320801,0.0848546,0.268505,0.00032273,0.000100774,0.00660075,4.94005e-05,0.000360113,0.00200553,0.112199,0.150351,0.00704756,0.199405,0.121709,5.8604e-06,0.0759036,0.350158,8.40838e-08,0.0491142,0.000378855,0.0541957,0.0883058,0.00246868,0.0187949,0.00894857,0.00265053,0.0450707,0.00142948,0.0235108,0.132631,0.0447483,0.000368532,0.0748174,0.0174545,0.110194,0.215858,1.18126e-06,0.182323,0.00660477,0.134107,0.000153866,0.119051,0.0196757,0.110868,0.175735,1.75603e-06,0.0985137,0.0755515,0.0302655,0.164103,0.141472,0.085537,0.0730922,0.0438087,0.0052702,0.0302521,0.0146861,0.262198,0.202388,0.0346699,0.0913381,0.129544,0.110696,0.0515825,0.000742211,0.258146,0.0186533,0.0296391,0.0352845,0.0565357,0.153577,0.0984158,0.000452009,9.88091e-07,0.0447121,0.291455,0.000358967,2.73079e-05,0.192028,0.0686515,0.149398,0.0530169,0.166112,0.0534404,0.0898401,0.2321,0.179282,0.052046,0.00262089,0.105131,0.118265,0.0177884,9.14943e-06,0.230552,0.0011332,0.205973,0.159869,0.0363736,0.000647611,4.17518e-06,0.155237,0.236268,0.0532055,0.108938,0.00014203,0.140245,0.0318635,0.160458,0.292792,0.147332,0.0622664,0.102951,8.92606e-05,0.0891668,0.14349,0.117261,0.0797088,0.0408965,0.0799774,6.58076e-08,0.329956,0.0094037,0.197158,1.7904e-05,0.0288641,0.0606832,0.00979559,0.0132285,0.147626,0.00174837,0.000127239,0.21271,0.132273,0.0830988,0.134907,0.184613,4.70224e-05,0.202467,0.208718,0.0972471,3.82975e-05,0.180711,0.112956,0.0797807,0.0790532,0.675167,0.476758,0.0553945,0.10068,0.125804,0.122288,0.0624687,1.30277e-08,0.21183,0.275612,0.235571,0.112872,0.128998,0.00619501,0.000659859,0.178155,0.00022309,0.146021,4.73345e-05,0.15291,0.0229006,0.238926,0.00279479,0.128521,0.1286,0.207017,1.93279e-05,0.259646,0.0916845,0.324438,0.0816983,0.226367,0.00187805,0.0147999,0.0457509,0.106603,0.106727,0.12083,0.000691559,0.0993998,0.00105579,0.0834863,0.324356,0.545829,0.113754,0.0504034,0.169684,3.14434e-05,0.0880794,0.603871,0.00265417,0.005515,0.00268757,0.000462571,0.420045,0.0114582,2.461e-07,0.545329,0.00385231,0.0881702,4.833e-07,0.017212,0.00499259,0.017023,0.000658513,0.364388,0.34505,0.369161,0.500422,0.147194,0.323639,0.123196,1.0694e-05,0.0232022,9.12245e-06,0.520726,0.143893,0.41477,0.279946,0.00704767,0.0262654,0.563725,0.164225,0.019108,0.257158,0.460819,0.511459,0.586668,0.322903,0.350886,0.0128438,0.583749,1.54946e-05,0.0455719,0.0151426,0.34907,0.359128,0.395864,0.318966,0.368633,1.95503e-05,0.0292801,0.512763,0.369971,0.578349,0.537928,0.00386096,0.109673,0.000322852,0.0301914,0.225357,0.199727,0.0113727,0.00100746,0.0510948,6.15009e-10,0.432689,1.36606e-07,7.80963e-05,0.0442147,0.606382,0.250139,0.258511,0.316925,0.356561,0.00185814,0.0241359,2.83778e-06,0.0962508,0.0310083,0.122819,0.128535,0.000207668,0.508325,0.000870154,0.651927,0.656755,0.046332,0.280307,0.393583,0.076625,0.0596868,0.000171467,0.293026,0.16661,0.694744,0.0678767,0.372182,0.0194133,0.214741,0.00124605,0.0166186,0.453022,0.35234,0.00195994,0.172079,8.57347e-08,0.421082,0.00024502,0.202782,0.103116,1.15782e-05,0.0594062,0.517001,0.620475,0.266107,0.0023737,0.188259,0.0191441,0.00443112,0.131612,0.00134091,0.198922,0.321282,0.00152374,0.0616078,0.178485,0.0615778,4.96064e-05,0.129238,0.651295,0.0793782,0.360161,0.429696,0.000154106,0.385297,0.706685,5.4074e-05,7.66545e-05,0.360203,0.00825487,3.67396e-05,0.289666,8.43885e-06,0.513045,0.452694,0.00168732,0.119811,0.265037,0.629795,0.0543569,0.000146586,0.0664979,0.002507,0.0236936,0.0727712,6.11293e-05,0.55524,0.624689,0.000100109,0.304719,4.10915e-06,9.84377e-08,0.00297491,0.117049,0.0786167,9.71948e-06,6.73434e-05,0.111753,0.64428,0.436806,0.576549,0.0330909,0.396083,7.385e-05,0.397546,0.0919254,0.0735469,0.248103,0.102621,0.0760107,0.187642,0.286156,0.261868,0.541583,0.0442046,0.247151,0.146385,8.40011e-06,0.0576261,0.000145336,0.164977,0.175633,0.139918,0.0685737,0.0828344,5.0158e-06,0.0238089,0.0851202,0.354433,0.00468928,0.0614918,0.219485,0.149782,0.136923,0.118103,0.113892,0.207214,1.92311e-05,0.0580534,0.00518407,8.86444e-10,0.0150478,0.0403091,0.000225021,2.84456e-05,0.0660736,0.108971,0.0879235,0.00263193,0.145546,0.28124,0.102433,0.251882,0.172263,0.243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}}
}}

Revision as of 15:31, 26 November 2012


Full id: C2464_lymphoma_acute_occipital_Neurons_cerebellum_small_parietal



Phase1 CAGE Peaks

Hg19::chr18:52988952..52988965,-p23@TCF4
Hg19::chr18:52988979..52988993,-p18@TCF4
Hg19::chr18:52989001..52989030,-p10@TCF4
Hg19::chr18:52989031..52989079,-p2@TCF4


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><br>

Cell Type
Ontology termp-valuen
lymphocyte of B lineage1.16e-1324
pro-B cell1.16e-1324
B cell2.65e-0814
Uber Anatomy
Ontology termp-valuen
adult organism8.17e-30114
nervous system1.01e-2589
central nervous system7.51e-2481
neural tube5.92e-2156
neural rod5.92e-2156
future spinal cord5.92e-2156
neural keel5.92e-2156
brain2.89e-2068
future brain2.89e-2068
regional part of nervous system7.98e-2053
regional part of brain7.98e-2053
regional part of forebrain3.80e-1841
forebrain3.80e-1841
anterior neural tube3.80e-1841
future forebrain3.80e-1841
ectoderm-derived structure1.75e-17171
ectoderm1.75e-17171
presumptive ectoderm1.75e-17171
neurectoderm1.69e-1686
telencephalon4.39e-1634
brain grey matter7.13e-1634
gray matter7.13e-1634
cerebral hemisphere2.83e-1532
regional part of telencephalon2.99e-1532
structure with developmental contribution from neural crest4.59e-15132
neural plate6.18e-1582
presumptive neural plate6.18e-1582
cerebral cortex3.31e-1325
pallium3.31e-1325
tissue4.89e-13773
regional part of cerebral cortex1.33e-1222
neocortex1.71e-1120
ecto-epithelium4.28e-11104
pre-chordal neural plate1.13e-1061
organ system subdivision3.70e-08223
anatomical cluster1.60e-07373


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)

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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
BCL3#602434.54710280373837.01262157705428e-073.14871532625096e-05
EBF1#187948.9064668465690.00015887907472010.00199629110739804
ELF1#199744.258097958807540.003041525565781240.016088628877868
EP300#203346.77394172622320.0004748459821442640.00434259540535594
JUND#372746.994663941871030.000417684217818580.00391654893380811
MAFK#7975427.10073313782991.85228494563408e-066.84781548449834e-05
NFKB1#479045.488063424193840.001102199566301980.0076792942298207
PAX5#507946.669565531177830.0005052774169483260.0044374931171095
POU2F2#545249.106124057742520.000145395665174930.00188375857526417
TAF1#687243.343046285745290.008005664898701650.0322185517458095
TBP#690843.706770687096390.005296377814784350.0244183288128841
YY1#752844.911170749853860.00171871838055440.0106852329868874
ZNF263#1012748.221841637010680.0002187871180958320.00248828354860183



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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