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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:44, 17 September 2013


Full id: C1431_CD4_Burkitt_CD8_diffuse_tonsil_spleen_lymphoma



Phase1 CAGE Peaks

Hg19::chr17:37917880..37917904,-p1@AK128436
Hg19::chr17:37921587..37921593,-p@chr17:37921587..37921593
-
Hg19::chr17:37934188..37934202,-p8@IKZF3
Hg19::chr17:37934204..37934241,-p3@IKZF3
Hg19::chr17:37934268..37934277,-p10@IKZF3
Hg19::chr17:37934280..37934299,-p6@IKZF3


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>disease_data<br>

Cell Type
Ontology termp-valuen
lymphocyte2.83e-6953
common lymphoid progenitor2.83e-6953
lymphoid lineage restricted progenitor cell1.61e-6752
nucleate cell4.06e-6655
nongranular leukocyte5.04e-38115
leukocyte1.36e-35136
lymphocyte of B lineage1.15e-3324
pro-B cell1.15e-3324
hematopoietic lineage restricted progenitor cell5.52e-31120
T cell1.08e-2925
pro-T cell1.08e-2925
mature alpha-beta T cell1.53e-2718
alpha-beta T cell1.53e-2718
immature T cell1.53e-2718
mature T cell1.53e-2718
immature alpha-beta T cell1.53e-2718
hematopoietic cell7.89e-26177
hematopoietic stem cell5.04e-25168
angioblastic mesenchymal cell5.04e-25168
hematopoietic oligopotent progenitor cell1.47e-22161
hematopoietic multipotent progenitor cell1.47e-22161
B cell1.42e-1914
CD8-positive, alpha-beta T cell4.85e-1811
CD4-positive, alpha-beta T cell4.60e-106
circulating cell3.50e-096
Uber Anatomy
Ontology termp-valuen
blood6.12e-1915
haemolymphatic fluid6.12e-1915
organism substance6.12e-1915
hemopoietic organ1.39e-107
immune organ1.39e-107
hemolymphoid system2.84e-07108
hematopoietic system2.97e-0798
blood island2.97e-0798
adult organism8.16e-07114
thymus9.97e-074
hemolymphoid system gland9.97e-074
thymic region9.97e-074
pharyngeal gland9.97e-074
thymus primordium9.97e-074
Disease
Ontology termp-valuen
lymphoma9.18e-1210


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)
MA0003.10.00461978
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.12.15903
MA0031.10.871496
MA0038.12.69832
MA0040.10.955415
MA0041.12.41676
MA0042.15.82512
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
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
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
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
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
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
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
MA0136.11.61362
MA0139.10.226048
MA0140.10.622527
MA0141.11.15452
MA0142.11.95656
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.21.80563
MA0018.20.709805
MA0099.20.629739
MA0079.20.000444266
MA0102.21.58513
MA0258.10.289793
MA0259.11.6038
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
BATF#10538416.23853452820243.98325915717398e-050.00074220803410543
BCL11A#53335418.91297006907142.18517293116183e-050.000480659805723695
IRF4#3662414.60967512449616.03404227507469e-050.000991331353101346
MEF2A#4205412.4954872730960.0001113336277199790.00154621977997964
NFKB1#479043.658708949462560.01207927289015230.0438326389414758
SPI1#668856.836936257102270.0001449641773974030.00188588860528244



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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