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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:38, 17 September 2013


Full id: C1132_thymus_CD4_CD8_Natural_chronic_acute_Peripheral



Phase1 CAGE Peaks

Hg19::chr11:118175596..118175612,+p3@CD3E
Hg19::chr11:118186215..118186232,+p@chr11:118186215..118186232
+
Hg19::chr11:118186261..118186272,+p@chr11:118186261..118186272
+
Hg19::chr11:118186324..118186363,+p@chr11:118186324..118186363
+
Hg19::chr11:118186366..118186415,+p@chr11:118186366..118186415
+
Hg19::chr11:118186552..118186562,+p@chr11:118186552..118186562
+
Hg19::chr11:60780935..60780941,+p@chr11:60780935..60780941
+


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
T cell1.30e-4525
pro-T cell1.30e-4525
mature alpha-beta T cell1.25e-4318
alpha-beta T cell1.25e-4318
immature T cell1.25e-4318
mature T cell1.25e-4318
immature alpha-beta T cell1.25e-4318
CD8-positive, alpha-beta T cell1.90e-2711
lymphoid lineage restricted progenitor cell4.58e-2552
lymphocyte1.87e-2453
common lymphoid progenitor1.87e-2453
nucleate cell2.66e-2355
CD4-positive, alpha-beta T cell1.44e-156
nongranular leukocyte3.47e-14115
leukocyte1.33e-13136
hematopoietic lineage restricted progenitor cell3.42e-10120
hematopoietic stem cell2.35e-09168
angioblastic mesenchymal cell2.35e-09168
natural killer cell5.38e-093
pro-NK cell5.38e-093
single nucleate cell1.48e-083
mononuclear cell1.48e-083
hematopoietic cell1.86e-08177
naive T cell3.51e-083
hematopoietic oligopotent progenitor cell4.46e-07161
hematopoietic multipotent progenitor cell4.46e-07161
Uber Anatomy
Ontology termp-valuen
blood3.95e-1515
haemolymphatic fluid3.95e-1515
organism substance3.95e-1515
hemopoietic organ2.08e-127
immune organ2.08e-127
thymus9.92e-114
hemolymphoid system gland9.92e-114
thymic region9.92e-114
pharyngeal gland9.92e-114
thymus primordium9.92e-114
pharyngeal epithelium3.90e-076


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)
MA0003.10.110456
MA0004.10.502801
MA0006.10.904424
MA0007.10.483857
MA0009.10.973289
MA0014.10.610358
MA0017.11.75854
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.940207
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.12.20119
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.11.46532
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.11.95014
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.11.14351
MA0113.10.665691
MA0114.11.36091
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.11.491
MA0139.13.11235
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.581146
MA0146.10.0610556
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.563664
MA0035.20.564239
MA0039.20.0170091
MA0138.20.704862
MA0002.20.213296
MA0137.20.95459
MA0104.20.223944
MA0047.20.636643
MA0112.22.55032
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.11.89358
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.11.34201
MA0161.10
MA0162.10.25944
MA0163.10.19677
MA0164.10.678332
MA0080.21.63199
MA0018.20.650405
MA0099.20.572
MA0079.20.00447823
MA0102.21.51913
MA0258.11.97124
MA0259.10.289405
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
CTCF#1066453.828754552196450.003387371192681340.0172909902244598
FOXA1#316946.332239856791690.001854681016920170.0109429428126165
GATA3#2625311.67279272451690.001549108698473610.0098440744362571
RAD21#588557.39645278246880.0001491014505228370.00192318221454299



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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