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Coexpression cluster:C3847: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00109922399700643!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00915261019990416!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462389044133549!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00136660501285327!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156795074719042!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00629399153325635!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329465658075082
|tf_chipseq_enrich=BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00109922399700643!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00915261019990416!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462389044133549!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00136660501285327!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156795074719042!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00629399153325635!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329465658075082
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,1.54465,0.667627,1.17594,0.575162,1.14835,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,2.67779,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,0.718382,0.63803,1.44641,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,2.8077,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,1.24629,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,1.34254,1.54991,2.35823,0.450952,1.27663,1.05794,1.68795,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,2.2314,1.70203,1.12965,0.930979,1.2374,1.48578,2.36206,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,3.0882,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,2.04753,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 16:23, 26 November 2012


Full id: C3847_CD4_NK_CD14_Eosinophils_CD8_Peripheral_Natural



Phase1 CAGE Peaks

Hg19::chr1:111418184..111418197,+p@chr1:111418184..111418197
+
Hg19::chr1:111418209..111418214,+p@chr1:111418209..111418214
+
Hg19::chr1:111418230..111418239,+p@chr1:111418230..111418239
+


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
leukocyte1.73e-46136
nongranular leukocyte6.89e-46115
hematopoietic cell2.03e-43177
hematopoietic stem cell6.89e-42168
angioblastic mesenchymal cell6.89e-42168
hematopoietic lineage restricted progenitor cell2.52e-41120
hematopoietic oligopotent progenitor cell9.48e-40161
hematopoietic multipotent progenitor cell9.48e-40161
T cell3.70e-3325
pro-T cell3.70e-3325
mature alpha-beta T cell2.84e-3118
alpha-beta T cell2.84e-3118
immature T cell2.84e-3118
mature T cell2.84e-3118
immature alpha-beta T cell2.84e-3118
lymphoid lineage restricted progenitor cell5.01e-2852
lymphocyte2.50e-2753
common lymphoid progenitor2.50e-2753
nucleate cell5.24e-2655
classical monocyte1.75e-2042
CD14-positive, CD16-negative classical monocyte1.75e-2042
CD8-positive, alpha-beta T cell7.29e-1811
myeloid leukocyte1.21e-1772
defensive cell4.31e-1748
phagocyte4.31e-1748
myeloid lineage restricted progenitor cell2.80e-1566
monopoietic cell3.96e-1559
monocyte3.96e-1559
monoblast3.96e-1559
promonocyte3.96e-1559
granulocyte monocyte progenitor cell6.06e-1567
myeloid cell7.05e-15108
common myeloid progenitor7.05e-15108
macrophage dendritic cell progenitor2.04e-1461
CD4-positive, alpha-beta T cell5.85e-136
circulating cell6.24e-126
mesenchymal cell1.47e-10354
connective tissue cell4.91e-10361
motile cell3.23e-08386
naive T cell1.51e-073
natural killer cell4.31e-073
pro-NK cell4.31e-073
stuff accumulating cell9.32e-0787
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.35e-2498
blood island7.35e-2498
hemolymphoid system1.33e-20108
immune system1.03e-1293
bone marrow2.44e-1276
blood8.91e-1215
haemolymphatic fluid8.91e-1215
organism substance8.91e-1215
bone element6.22e-1182
skeletal element2.30e-0990
connective tissue2.51e-09371
skeletal system8.79e-08100


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-050.00109922399700643
EBF1#187938.9064668465690.00141523283560980.00915261019990416
ELF1#199734.258097958807540.01295179875054610.0462389044133549
IRF4#3662321.91451268674419.49854535978121e-050.00136660501285327
JUND#372736.994663941871030.002921845042734990.0156795074719042
TCF12#6938310.63446490218640.0008313523990202070.00629399153325635
YY1#752834.911170749853860.008441455341808260.0329465658075082



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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