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Coexpression cluster:C4397: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190719443895586!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662131173745373!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326880793356392!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00438325349847124!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323684373356564!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321849659404119!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764178257610968!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388929396899317!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392785631098717!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108992892356223!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128520073370417!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187169182847099!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.0072205722391354!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270435488162502!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00472679846221779!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277766770495162!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247482771586984
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190719443895586!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662131173745373!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326880793356392!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00438325349847124!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323684373356564!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321849659404119!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764178257610968!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388929396899317!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392785631098717!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108992892356223!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128520073370417!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187169182847099!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.0072205722391354!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270435488162502!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00472679846221779!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277766770495162!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247482771586984
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,1.54465,1.60265,1.17594,0.575162,0.452865,0.305559,0.69094,1.26332,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,0.439574,1.46099,0.137917,0.596053,0.855276,1.39264,0.469078,0.598234,1.82956,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,2.18821,1.60305,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,2.0644,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,3.76231,0.82001,0.381882,2.39382,2.0169,1.63834,1.36973,2.75673,0.543775,0.642354,1.37703,0.450952,1.27663,1.05794,0.360456,2.38768,1.22626,1.27082,1.1798,1.09802,3.17067,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,2.50498,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,2.36206,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,2.48899,0.883164,1.08214,2.31409,0.773313,0.539692,1.54007,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135
}}
}}

Revision as of 16:43, 26 November 2012


Full id: C4397_acute_chronic_NK_Hodgkin_thymus_glioblastoma_non



Phase1 CAGE Peaks

Hg19::chr4:178231020..178231036,+p1@NEIL3
Hg19::chr4:178231053..178231065,+p2@NEIL3
Hg19::chr4:178231084..178231093,+p4@NEIL3


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><br>disease_data<br>


Cell Type
Ontology termp-valuen
animal cell7.22e-12679
eukaryotic cell7.22e-12679
epithelial cell1.59e-10253
native cell9.13e-09722
Disease
Ontology termp-valuen
cancer4.61e-45235
disease of cellular proliferation8.39e-45239
hematologic cancer1.30e-2551
immune system cancer1.30e-2551
organ system cancer6.30e-24137
leukemia1.48e-1939
cell type cancer2.02e-17143
myeloid leukemia1.79e-1431
carcinoma5.73e-14106
lymphoma3.43e-0710


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#90536.336201576962630.003930750035764890.0190719443895586
CHD2#1106310.34402283411690.0009033701102746880.00662131173745373
E2F1#186934.907389214879320.008460985347239390.0326880793356392
E2F4#1874312.66806031528440.0004917987006298980.00438325349847124
E2F6#187635.017155731697390.00791769806886330.0323684373356564
EGR1#195834.988179094810140.008056488137383440.0321849659404119
ETS1#211339.728760922202340.001085840092584840.00764178257610968
GATA1#2623313.56030814380040.0004009615963782630.00388929396899317
HDAC2#3066313.41562023662630.0004140761399857210.00392785631098717
HMGN3#932438.178547723350590.001827766942164210.0108992892356223
IRF1#365937.63716375356390.002244692747297240.0128520073370417
MAX#414936.452555509007120.003721913834265510.0187169182847099
MXI1#460139.96157162875930.001011470541259020.0072205722391354
NFKB1#479035.488063424193840.006049381815655430.0270435488162502
NRF1#4899312.21027944771090.0005492172401020010.00472679846221779
SIN3A#2594235.408884726815140.006318961977991520.0277766770495162
SP1#666735.69838137814090.005403962701712170.0247482771586984



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.