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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 12:07, 17 September 2013


Full id: C2526_acute_CD14_CD14CD16_Whole_CD4_biphenotypic_Dendritic



Phase1 CAGE Peaks

Hg19::chr1:151129103..151129130,+p2@TNFAIP8L2
Hg19::chr1:151129135..151129165,+p1@TNFAIP8L2
Hg19::chr8:22437965..22438000,+p3@PDLIM2
Hg19::chr8:22438009..22438035,+p4@PDLIM2


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
hematopoietic stem cell1.94e-90168
angioblastic mesenchymal cell1.94e-90168
hematopoietic oligopotent progenitor cell4.80e-86161
hematopoietic multipotent progenitor cell4.80e-86161
hematopoietic cell3.85e-84177
leukocyte6.64e-73136
hematopoietic lineage restricted progenitor cell2.54e-63120
nongranular leukocyte5.79e-62115
myeloid cell2.31e-58108
common myeloid progenitor2.31e-58108
myeloid leukocyte1.70e-4272
granulocyte monocyte progenitor cell9.52e-3967
myeloid lineage restricted progenitor cell3.07e-3866
macrophage dendritic cell progenitor1.78e-3661
monopoietic cell9.31e-3659
monocyte9.31e-3659
monoblast9.31e-3659
promonocyte9.31e-3659
defensive cell1.17e-3048
phagocyte1.17e-3048
classical monocyte4.90e-2642
CD14-positive, CD16-negative classical monocyte4.90e-2642
nucleate cell2.73e-2355
lymphocyte9.89e-2353
common lymphoid progenitor9.89e-2353
lymphoid lineage restricted progenitor cell2.37e-2252
mesenchymal cell3.19e-14354
T cell2.32e-1325
pro-T cell2.32e-1325
connective tissue cell5.68e-13361
mature alpha-beta T cell3.21e-1118
alpha-beta T cell3.21e-1118
immature T cell3.21e-1118
mature T cell3.21e-1118
immature alpha-beta T cell3.21e-1118
lymphocyte of B lineage3.38e-0924
pro-B cell3.38e-0924
motile cell7.73e-09386
stuff accumulating cell1.88e-0887
intermediate monocyte3.12e-089
CD14-positive, CD16-positive monocyte3.12e-089
CD8-positive, alpha-beta T cell4.78e-0811
B cell8.25e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.90e-4498
blood island8.90e-4498
hemolymphoid system1.30e-38108
bone marrow7.12e-3276
immune system1.44e-3093
bone element4.96e-3082
skeletal element5.27e-2690
skeletal system3.52e-21100
adult organism4.26e-17114
connective tissue1.04e-11371
lateral plate mesoderm1.99e-10203
blood7.44e-0915
haemolymphatic fluid7.44e-0915
organism substance7.44e-0915
Disease
Ontology termp-valuen
leukemia2.14e-1839
hematologic cancer1.17e-1751
immune system cancer1.17e-1751
myeloid leukemia2.51e-1531


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.11.66718
MA0051.11.91805
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.11.8408
MA0072.11.1744
MA0073.10.214613
MA0074.11.91637
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.11.43218
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.11.94315
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.12.87436
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.11.37853
MA0164.10.90014
MA0080.22.27911
MA0018.20.870662
MA0099.20.7872
MA0079.20.869502
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#1066445.360256373075030.001211145381643620.00817546616555573



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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