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Coexpression cluster:C1420: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:44, 17 September 2013


Full id: C1420_CD4_acute_Hodgkin_chronic_thymus_CD8_Whole



Phase1 CAGE Peaks

Hg19::chr16:30390783..30390810,-p@chr16:30390783..30390810
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Hg19::chr7:142498799..142498808,+p5@AJ568018
Hg19::chr7:142498836..142498876,-p@chr7:142498836..142498876
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Hg19::chr7:142498988..142499010,-p@chr7:142498988..142499010
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Hg19::chr7:142499055..142499068,-p@chr7:142499055..142499068
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Hg19::chr7:142499841..142499860,-p@chr7:142499841..142499860
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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
lymphocyte3.28e-4853
common lymphoid progenitor3.28e-4853
lymphoid lineage restricted progenitor cell1.31e-4652
nucleate cell4.98e-4655
T cell5.04e-4625
pro-T cell5.04e-4625
mature alpha-beta T cell1.12e-3618
alpha-beta T cell1.12e-3618
immature T cell1.12e-3618
mature T cell1.12e-3618
immature alpha-beta T cell1.12e-3618
CD8-positive, alpha-beta T cell8.31e-2311
nongranular leukocyte1.02e-20115
leukocyte5.47e-18136
hematopoietic lineage restricted progenitor cell6.95e-15120
CD4-positive, alpha-beta T cell1.17e-136
hematopoietic cell2.04e-13177
hematopoietic stem cell4.01e-13168
angioblastic mesenchymal cell4.01e-13168
hematopoietic oligopotent progenitor cell9.83e-11161
hematopoietic multipotent progenitor cell9.83e-11161
circulating cell2.51e-086
naive T cell1.17e-073
natural killer cell3.47e-073
pro-NK cell3.47e-073
single nucleate cell5.51e-073
mononuclear cell5.51e-073
Uber Anatomy
Ontology termp-valuen
blood1.05e-1715
haemolymphatic fluid1.05e-1715
organism substance1.05e-1715
hemopoietic organ9.81e-117
immune organ9.81e-117
thymus1.30e-094
hemolymphoid system gland1.30e-094
thymic region1.30e-094
pharyngeal gland1.30e-094
thymus primordium1.30e-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)
MA0003.10.176622
MA0004.11.37419
MA0006.10.391183
MA0007.11.33289
MA0009.11.03681
MA0014.10.262822
MA0017.11.935
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.11.16137
MA0059.12.01959
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.11.59928
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00563817
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.11.29635
MA0093.11.80532
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.993014
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.11.25994
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.86787
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.13.48752
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.21.22729
MA0035.20.621793
MA0039.20.0313803
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.21.65732
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.0607789
MA0102.21.58513
MA0258.10.788656
MA0259.10.336472
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
THAP1#55145315.68457230142570.0006023469800864850.00503147374656102
USF1#739144.240999518138640.007005367750829420.0296040140215616
ZBTB7A#5134144.901272871917260.004079628118843750.0194873893662606



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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