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Coexpression cluster:C4259: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00110073138935339!BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000778761876696641!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321566752495677!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00137038068632434!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195203588894872!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270238841458248!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173325695152301!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666051000036189!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165586915396347!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00309868288103302
|tf_chipseq_enrich=BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00110073138935339!BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000778761876696641!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321566752495677!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00137038068632434!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195203588894872!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270238841458248!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173325695152301!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666051000036189!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165586915396347!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00309868288103302
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0.0107847
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,1.74644,0.459024,1.14559,2.20639,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,1.39614,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,2.52363,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 16:38, 26 November 2012


Full id: C4259_NK_CD4_B_anaplastic_CD8_Mast_plasma



Phase1 CAGE Peaks

Hg19::chr3:105895720..105895729,+p@chr3:105895720..105895729
+
Hg19::chr3:105895792..105895806,+p@chr3:105895792..105895806
+
Hg19::chr3:105895821..105895830,+p@chr3:105895821..105895830
+


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
lymphoid lineage restricted progenitor cell6.66e-3652
lymphocyte3.78e-3553
common lymphoid progenitor3.78e-3553
nucleate cell1.01e-3355
T cell6.15e-2625
pro-T cell6.15e-2625
mature alpha-beta T cell1.17e-1918
alpha-beta T cell1.17e-1918
immature T cell1.17e-1918
mature T cell1.17e-1918
immature alpha-beta T cell1.17e-1918
hematopoietic lineage restricted progenitor cell2.48e-18120
nongranular leukocyte2.34e-17115
leukocyte2.49e-17136
natural killer cell2.98e-173
pro-NK cell2.98e-173
CD8-positive, alpha-beta T cell3.86e-1311
hematopoietic stem cell3.91e-13168
angioblastic mesenchymal cell3.91e-13168
hematopoietic oligopotent progenitor cell1.62e-12161
hematopoietic multipotent progenitor cell1.62e-12161
regulatory T cell1.71e-122
CD4-positive, CD25-positive, alpha-beta regulatory T cell1.71e-122
naive regulatory T cell1.71e-122
hematopoietic cell3.16e-12177
naive T cell1.29e-083
innate effector T cell1.46e-071
immature NK T cell1.46e-071
effector T cell1.46e-071
mature NK T cell1.46e-071
immature NK T cell stage IV1.46e-071
immature NK T cell stage I1.46e-071
immature NK T cell stage II1.46e-071
immature NK T cell stage III1.46e-071
Disease
Ontology termp-valuen
lymphoma3.06e-0910
anemia5.45e-071
non-Hodgkin lymphoma6.88e-071
cutaneous T cell lymphoma6.88e-071
mycosis fungoides6.88e-071


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
BATF#10538324.35780179230366.91705216281876e-050.00110073138935339
BCL11A#53335328.36945510360714.37778126761649e-050.000778761876696641
EGR1#195834.988179094810140.008056488137383440.0321566752495677
IRF4#3662321.91451268674419.49854535978121e-050.00137038068632434
MEF2A#4205318.74323090964410.0001518243905622470.00195203588894872
NFKB1#479035.488063424193840.006049381815655430.0270238841458248
PAX5#507936.669565531177830.003370290999677260.0173325695152301
RAD21#5885310.35503389545630.0009004912073565420.00666051000036189
RXRA#6256320.07461713913330.0001235730348432220.00165586915396347
SMC3#9126315.04493284493280.0002935825420371870.00309868288103302



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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