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Coexpression cluster:C1624: Difference between revisions

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|id=C1624
|id=C1624
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:1240!1.91e-14!39;DOID:8692!4.60e-14!31;DOID:0050686!3.99e-12!137;DOID:2531!7.68e-11!51;DOID:0060083!7.68e-11!51;DOID:14566!1.00e-06!239
|ontology_enrichment_disease=DOID:1240!1.81e-13!39;DOID:8692!5.02e-13!31;DOID:0050686!8.82e-12!137;DOID:2531!1.10e-10!51;DOID:0060083!1.10e-10!51;DOID:14566!6.02e-07!239
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tf_chipseq_enrich=CCNT2#905;5:6.33620157696263:9.78880505817628e-05:0.00138847346390177!CHD2#1106;5:10.3440228341169:8.43981772346334e-06:0.000230022474744465!E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352155125233486!E2F6#1876;4:4.01372458535791:0.00663211823393388:0.0282865110562266!EGR1#1958;5:4.98817909481014:0.000323739800059071:0.00330379724236558!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.00572484177109251!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000388653491550753!GABPB1#2553;5:7.06768383618217:5.6685482528729e-05:0.000947834631735178!GATA1#2623;5:13.5603081438004:2.17950082879909e-06:7.83292797862863e-05!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.000101069313293392!HMGN3#9324;5:8.17854772335059:2.73180911341838e-05:0.000581310945387738!IRF3#3661;5:46.9819522114896:4.35776524686345e-09:3.54179489974452e-07!MAFK#7975;5:27.1007331378299:6.83095404221442e-08:4.15019202568256e-06!MXI1#4601;5:9.9615716287593:1.01894348670516e-05:0.00026644326191287!NANOG#79923;5:29.2447784810127:4.66760911383881e-08:3.03726123514151e-06!NFYA#4800;5:18.4255806998305:4.70418681889082e-07:2.2220740261336e-05!NFYB#4801;5:16.7597932535365:7.55590255814554e-07:3.32265645166384e-05!REST#5978;3:5.79001722967681:0.00946878869443394:0.0356865801471613!SP1#6667;5:5.6983813781409:0.00016639184371255:0.00204012652799895!SP2#6668;5:26.1535304938446:8.16125998835445e-08:4.87337811277159e-06!SREBF1#6720;5:47.0058494404883:4.34669369311096e-09:3.538303527785e-07!SRF#6722;4:11.0377426097342:0.000129925581484675:0.00170984095321043!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135125156089477!TFAP2A#7020;3:9.91118062382697:0.00202154697751128:0.0117437059063467!TFAP2C#7022;3:6.48553716591613:0.00685895151794:0.0290511005589316!THAP1#55145;5:31.3691446028513:3.28679666061441e-08:2.20894309162103e-06!TRIM28#10155;3:11.1543150271575:0.00143315927152925:0.00920074509215905!ZBTB7A#51341;5:7.3519093078759:4.65425347594289e-05:0.000815032828259556!ZNF263#10127;5:8.22184163701068:2.6606316672286e-05:0.000570465429467641
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0809,0.0898207,0.126545,0.0918749,0.0686325,0.0569043,0.0639461,0.387306,0.267408,0.312064,0.080156,0.274185,0.53753,0.0545112,0.160961,0.33844,0.0649137,0.0974216,0.595767,0.195675,0.174786,0.176557,0.396547,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.00239454,0.385962,0.334921,0.296227,0.208788,0.0104864,0.36304,2.75722e-05,0.123626,0.270619,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.223204,0.143824,0.460679,0.431098,0.0775891,0.153079,0.62577,0.211515,0.125701,0.175283,0.204954,0.209341,0.855975,0.0185433,0.084895,0.160115,0.0819954,0.10091,0.122658,0.151161,0.228398,0.056055,0.120552,0.41771,0.655862,0.529713,0.335207,0.434016,0.190688,0.000505851,0.278645,0.733648,0.0940982,0.0780533,0.564811,0.0993772,0.274769,0.448923,0.11602,0.344528,0.436413,0.0585992,0.20045,0.274438,0.0225031,0.000957949,0.319826,0.336512,0.173868,0.109708,0.174594,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.114361,0.347759,0.242462,0.0620267,0.211111,0.0738743,0.0882327,0.183058,0.150073,0.270522,0.16872,0.341388,0.0934526,0.359135,0.123404,0.0196604,0.0316547,0.3033,0.0643653,0.163542,0.483244,0.27134,0.500871,0.239667,0.10226,0.29809,0.0301117,0.00132511,0.245965,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.244789,0.267391,0.301441,0.21807,0.350528,0.382904,0.432408,0.190404,0.135865,0.488841,0.18137,0.180609,0.291283,0.273972,0.153023,0.400137,0.37958,0.22307,0.160699,0.391307,0.166736,0.181253,0.0422294,0.263877,0.146486,0.431348,0.262486,0.294204,0.00911376,0.288826,0.246621,0.463617,0.697373,0.0965376,0.377203,0.279263,0.336564,0.35463,0.581771,0.800557,0.0594155,0.587524,0.208795,0.0713793,0.212621,0.594469,0.1798,0.0791056,0.581874,0.355154,0.730614,0.251388,0.537088,0.603804,0.629445,0.306963,0.206759,0.526495,0.580285,0.550495,0.424482,0.820986,0.610475,0.00638184,0.561689,0.0269405,0.00125038,0.623136,0.708698,0.00950745,0.445257,0.349068,0.70429,0.798758,0.557035,0.427789,0.689998,0.386595,0.0700328,0.433702,0.258394,0.644878,0.432123,0.759415,0.661773,0.494975,0.0903515,0.0895484,0.259088,0.371758,0.71344,0.562417,0.183098,0.570752,0.254547,0.673352,0.821811,0.680843,0.500384,0.541378,0.47213,0.0243913,0.723387,0.898765,0.446908,0.315485,0.311289,0.0572024,0.4488,0.389888,0.603509,0.511254,0.553178,0.246387,0.224252,0.0603905,0.155054,0.466978,0.518234,0.257848,0.353942,0.192234,0.427276,0.00295893,0.466967,0.283682,0.424668,0.462212,0.474058,0.583101,0.702164,0.477016,0.263776,0.498956,0.00553884,0.55798,0.349033,0.0205893,0.723248,0.34194,0.592696,0.592314,0.27725,0.380115,0.763919,0.317485,0.633504,0.220564,0.845182,0.262394,0.307462,0.135076,0.469588,0.664443,0.274593,0.490712,0.541363,0.709432,0.583627,0.531474,0.720644,0.562305,0.0010781,0.361524,0.31558,0.412744,0.54408,0.62698,0.0367094,0.415367,1.14436e-05,0.45585,0.36864,0.538745,0.456862,0.453004,0.00116776,0.00964276,0.693441,0.382214,0.553161,0.639572,0.68995,0.339393,0.694478,0.306231,0.298354,0.646049,0.784543,0.457741,0.641611,0.426239,0.162155,0.289012,0.572661,0.412586,0.534679,0.41502,0.55475,0.66153,0.523749,0.499347,0.307426,0.206772,0.196912,0.490527,0.132075,0.44799,0.00173749,0.318338,0.276338,0.126433,0.417412,0.318174,0.0555558,0.295666,0.393022,0.293641,0.116969,0.401231,0.255983,0.297663,0.256708,0.338258,0.322052,0.145568,0.153833,0.261242,0.38389,0.54721,0.388459,0.321362,0.627637,0.280757,0.301366,0.340343,0.343265,0.0337506,0.462092,0.336254,0.308589,0.291523,0.19697,0.309816,0.0537285,0.15063,0.0210584,0.281455,0.348739,0.419895,0.138495,0.208834,0.0587417,0.377566,0.342366,0.109684,0.322704,0.403482,0.181288,0.230841,0.352328,0.255358,0.351665,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.312881,0.0365105,0.244656,0.192188,0.158985,0.174153,0.0972854,0.333309,0.249919,0.339517,0.303699,0.198326,0.0144647,0.0244644,0.282501,0.252005,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.117618,0.392533,0.396962,0.316002,0.330317,0.0582923,0.225079,0.050521,0.379651,0.185715,0.345505,0.375521,0.271405,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.343014,0.270094,0.276922,0.156279,0.313647,0.461742,0.10563,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.0354176,0.224871,0.398887,0.088016,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.0753413,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.297596,0.42392,0.425912,0.380826,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,0.13907,0.470121,0.269432,0.250466,0.409882,0.115686,0.408975,0.162633,0.342661,0.27567,0.248127,0.33299,0.384731,0.319112,0.526476
}}
}}

Revision as of 11:31, 19 October 2012


Full id: C1624_parotid_submaxillary_Mast_chronic_mesenchymal_acute_non



Phase1 CAGE Peaks

Hg19::chr11:17298255..17298296,+p2@NUCB2
Hg19::chr11:17298297..17298341,+p1@NUCB2
Hg19::chr11:17298342..17298353,+p4@NUCB2
Hg19::chr11:17298522..17298531,+p5@NUCB2
Hg19::chr11:17298543..17298588,+p3@NUCB2


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
leukemia1.81e-1339
myeloid leukemia5.02e-1331
organ system cancer8.82e-12137
hematologic cancer1.10e-1051
immune system cancer1.10e-1051
disease of cellular proliferation6.02e-07239


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
CCNT2#90556.336201576962639.78880505817628e-050.00138847346390177
CHD2#1106510.34402283411698.43981772346334e-060.000230022474744465
E2F1#186954.907389214879320.0003512818099256460.00352155125233486
E2F6#187644.013724585357910.006632118233933880.0282865110562266
EGR1#195854.988179094810140.0003237398000590710.00330379724236558
ELF1#199754.258097958807540.0007142416939776840.00572484177109251
FOS#235358.99795530889441.69470025615156e-050.000388653491550753
GABPB1#255357.067683836182175.6685482528729e-050.000947834631735178
GATA1#2623513.56030814380042.17950082879909e-067.83292797862863e-05
GATA2#2624512.7449317335542.9719152914525e-060.000101069313293392
HMGN3#932458.178547723350592.73180911341838e-050.000581310945387738
IRF3#3661546.98195221148964.35776524686345e-093.54179489974452e-07
MAFK#7975527.10073313782996.83095404221442e-084.15019202568256e-06
MXI1#460159.96157162875931.01894348670516e-050.00026644326191287
NANOG#79923529.24477848101274.66760911383881e-083.03726123514151e-06
NFYA#4800518.42558069983054.70418681889082e-072.2220740261336e-05
NFYB#4801516.75979325353657.55590255814554e-073.32265645166384e-05
REST#597835.790017229676810.009468788694433940.0356865801471613
SP1#666755.69838137814090.000166391843712550.00204012652799895
SP2#6668526.15353049384468.16125998835445e-084.87337811277159e-06
SREBF1#6720547.00584944048834.34669369311096e-093.538303527785e-07
SRF#6722411.03774260973420.0001299255814846750.00170984095321043
TAF1#687253.343046285745290.002394600090870310.0135125156089477
TFAP2A#702039.911180623826970.002021546977511280.0117437059063467
TFAP2C#702236.485537165916130.006858951517940.0290511005589316
THAP1#55145531.36914460285133.28679666061441e-082.20894309162103e-06
TRIM28#10155311.15431502715750.001433159271529250.00920074509215905
ZBTB7A#5134157.35190930787594.65425347594289e-050.000815032828259556
ZNF263#1012758.221841637010682.6606316672286e-050.000570465429467641



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1624&oldid=2247641"