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{{Coexpression_clusters
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|full_id=C476_thymus_acute_Hodgkin_CD4_CD8_chronic_vein
|id=C476
|ontology_enrichment_celltype=CL:0000738!1.98e-23!140;CL:0002087!4.17e-18!119;CL:0000542!4.34e-18!53;CL:0000051!4.34e-18!53;CL:0000838!8.41e-18!52;CL:0002031!1.46e-15!124;CL:0000037!2.77e-14!172;CL:0000566!2.77e-14!172;CL:0000988!1.77e-13!182;CL:0000084!2.02e-13!25;CL:0000827!2.02e-13!25;CL:0002032!2.18e-12!165;CL:0000837!2.18e-12!165;CL:0000791!2.99e-12!18;CL:0000789!2.99e-12!18;CL:0002420!2.99e-12!18;CL:0002419!2.99e-12!18;CL:0000790!2.99e-12!18;CL:0000625!7.73e-09!11
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.69e-17!115;UBERON:0000178!8.37e-09!15;UBERON:0000179!8.37e-09!15;UBERON:0000463!8.37e-09!15;UBERON:0002390!2.69e-07!102;UBERON:0003061!2.69e-07!102
}}

Latest revision as of 11:23, 17 September 2013


Full id: C476_thymus_acute_Hodgkin_CD4_CD8_chronic_vein



Phase1 CAGE Peaks

Hg19::chr11:118209551..118209563,+p@chr11:118209551..118209563
+
Hg19::chr11:128344618..128344625,-p@chr11:128344618..128344625
-
Hg19::chr12:56324854..56324865,+p8@DGKA
Hg19::chr17:37309243..37309269,-p3@PLXDC1
Hg19::chr17:37309281..37309308,-p4@PLXDC1
Hg19::chr20:31097697..31097710,+p3@AK097865
Hg19::chr20:31097722..31097734,+p2@AK097865
Hg19::chr21:44597363..44597380,+p@chr21:44597363..44597380
+
Hg19::chr2:87036803..87036819,+p@chr2:87036803..87036819
+
Hg19::chr5:133450223..133450240,-p@chr5:133450223..133450240
-
Hg19::chr5:133451159..133451187,-p@chr5:133451159..133451187
-
Hg19::chr5:133451190..133451218,-p@chr5:133451190..133451218
-
Hg19::chr5:133451294..133451310,+p2@TCF7
Hg19::chr6:166825362..166825375,+p@chr6:166825362..166825375
+
Hg19::chr6:25442306..25442342,+p@chr6:25442306..25442342
+
Hg19::chr7:141998704..141998722,+p1@TRBV1
Hg19::chr7:55543402..55543436,+p@chr7:55543402..55543436
+
Hg19::chrX:123870889..123870903,-p@chrX:123870889..123870903
-
Hg19::chrX:123870918..123870949,-p@chrX:123870918..123870949
-
Hg19::chrX:123870951..123870959,-p@chrX:123870951..123870959
-


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
mature alpha-beta T cell1.85e-5418
alpha-beta T cell1.85e-5418
immature T cell1.85e-5418
mature T cell1.85e-5418
immature alpha-beta T cell1.85e-5418
T cell1.53e-4225
pro-T cell1.53e-4225
CD8-positive, alpha-beta T cell1.91e-3811
lymphoid lineage restricted progenitor cell5.62e-2552
lymphocyte2.12e-2453
common lymphoid progenitor2.12e-2453
nucleate cell2.59e-2355
CD4-positive, alpha-beta T cell5.30e-216
nongranular leukocyte7.62e-14115
leukocyte6.87e-12136
naive T cell3.12e-113
single nucleate cell8.21e-113
mononuclear cell8.21e-113
natural killer cell9.73e-113
pro-NK cell9.73e-113
hematopoietic lineage restricted progenitor cell1.23e-09120
hematopoietic stem cell1.98e-08168
angioblastic mesenchymal cell1.98e-08168
regulatory T cell6.90e-082
CD4-positive, CD25-positive, alpha-beta regulatory T cell6.90e-082
naive regulatory T cell6.90e-082
hematopoietic cell1.08e-07177
Uber Anatomy
Ontology termp-valuen
blood5.14e-2115
haemolymphatic fluid5.14e-2115
organism substance5.14e-2115
hemopoietic organ1.46e-127
immune organ1.46e-127
thymus3.09e-094
hemolymphoid system gland3.09e-094
thymic region3.09e-094
pharyngeal gland3.09e-094
thymus primordium3.09e-094


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)
MA0003.10.0831383
MA0004.11.02175
MA0006.10.0840255
MA0007.10.970384
MA0009.10.561062
MA0014.10.774885
MA0017.10.105116
MA0019.10.290278
MA0024.10.467291
MA0025.10.684106
MA0027.12.13512
MA0028.12.15449
MA0029.10.484339
MA0030.11.19426
MA0031.11.8859
MA0038.10.25521
MA0040.10.489524
MA0041.10.193578
MA0042.10.171628
MA0043.10.561349
MA0046.10.551181
MA0048.10.934089
MA0050.10.172223
MA0051.10.251994
MA0052.10.492957
MA0055.11.03933
MA0056.10
MA0057.10.395732
MA0058.11.24845
MA0059.11.81136
MA0060.10.0338613
MA0061.10.0254296
MA0063.10
MA0066.10.255535
MA0067.10.858361
MA0068.10.614744
MA0069.10.547689
MA0070.10.537571
MA0071.12.62683
MA0072.10.533514
MA0073.11.99222
MA0074.10.70075
MA0076.12.5597
MA0077.10.526569
MA0078.10.33032
MA0081.10.37884
MA0083.10.567893
MA0084.11.03923
MA0087.10.531309
MA0088.11.33115
MA0089.10
MA0090.10.427877
MA0091.10.182521
MA0092.10.157193
MA0093.11.01605
MA0095.10
MA0098.10
MA0100.10.265855
MA0101.10.294344
MA0103.10.970204
MA0105.10.0296587
MA0106.10.782788
MA0107.10.757938
MA0108.21.06707
MA0109.10
MA0111.10.449411
MA0113.10.300221
MA0114.10.0506063
MA0115.10.785493
MA0116.10.44115
MA0117.10.595385
MA0119.10.718217
MA0122.10.619196
MA0124.10.746208
MA0125.10.667416
MA0130.10
MA0131.10.345226
MA0132.10
MA0133.10
MA0135.10.588754
MA0136.10.721948
MA0139.10.730869
MA0140.10.224213
MA0141.11.23687
MA0142.10.39079
MA0143.10.300362
MA0144.12.01003
MA0145.11.1391
MA0146.10.166442
MA0147.10.449423
MA0148.10.198049
MA0149.10.21714
MA0062.22.48951
MA0035.20.223695
MA0039.20.42377
MA0138.20.331323
MA0002.21.24341
MA0137.20.654613
MA0104.20.317924
MA0047.20.277681
MA0112.20.0489386
MA0065.20.623555
MA0150.10.134443
MA0151.10
MA0152.10.229055
MA0153.10.65174
MA0154.10.538127
MA0155.10.204379
MA0156.10.660462
MA0157.10.367703
MA0158.10
MA0159.10.450931
MA0160.11.13321
MA0161.10
MA0162.10.0394051
MA0163.10.0436203
MA0164.10.834714
MA0080.20.605142
MA0018.20.288301
MA0099.20.229319
MA0079.20.45214
MA0102.21.07547
MA0258.10.0413436
MA0259.10.214864
MA0442.10



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
GATA3#262545.44730327144120.005486793888199380.0248465189649939
USF1#739182.544599710883180.007897848159016730.032420539418267



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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