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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:42, 17 September 2013


Full id: C1342_CD14_CD19_Eosinophils_Neutrophils_Peripheral_Natural_Basophils



Phase1 CAGE Peaks

Hg19::chr11:58346281..58346294,-p@chr11:58346281..58346294
-
Hg19::chr1:155108603..155108650,-p@chr1:155108603..155108650
-
Hg19::chr1:65532746..65532757,+p@chr1:65532746..65532757
+
Hg19::chr5:137879399..137879412,-p4@ETF1
Hg19::chr9:102581879..102581894,+p@chr9:102581879..102581894
+
Hg19::chrX:24167676..24167700,-p3@ZFX-AS1


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

GO IDGO nameFDR corrected p-value
GO:0016149translation release factor activity, codon specific0.00120687625103026
GO:0006449regulation of translational termination0.00241375250206052
GO:0043022ribosome binding0.00261489854389889
GO:0008079translation termination factor activity0.00261489854389889
GO:0006415translational termination0.00261489854389889
GO:0003747translation release factor activity0.00261489854389889
GO:0043021ribonucleoprotein binding0.00293098518107349
GO:0043624cellular protein complex disassembly0.00337925350288473
GO:0043241protein complex disassembly0.00337925350288473
GO:0032984macromolecular complex disassembly0.00337925350288473
GO:0022411cellular component disassembly0.0053760851182257
GO:0006417regulation of translation0.0173272947469344
GO:0031326regulation of cellular biosynthetic process0.0173272947469344
GO:0008135translation factor activity, nucleic acid binding0.0173272947469344
GO:0009889regulation of biosynthetic process0.0174594764315711
GO:0051246regulation of protein metabolic process0.0318313611209231



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
leukocyte6.36e-59136
hematopoietic stem cell3.53e-49168
angioblastic mesenchymal cell3.53e-49168
hematopoietic lineage restricted progenitor cell3.73e-48120
nongranular leukocyte6.76e-47115
hematopoietic cell4.11e-46177
hematopoietic oligopotent progenitor cell4.79e-45161
hematopoietic multipotent progenitor cell4.79e-45161
classical monocyte4.24e-4442
CD14-positive, CD16-negative classical monocyte4.24e-4442
myeloid leukocyte2.69e-3972
defensive cell1.47e-3648
phagocyte1.47e-3648
granulocyte monocyte progenitor cell2.12e-3367
macrophage dendritic cell progenitor2.62e-3161
myeloid lineage restricted progenitor cell1.21e-3066
monopoietic cell2.78e-2959
monocyte2.78e-2959
monoblast2.78e-2959
promonocyte2.78e-2959
myeloid cell1.28e-28108
common myeloid progenitor1.28e-28108
stuff accumulating cell5.66e-1887
mesenchymal cell2.72e-17354
connective tissue cell2.61e-16361
motile cell2.74e-16386
lymphoid lineage restricted progenitor cell5.20e-1552
lymphocyte1.56e-1453
common lymphoid progenitor1.56e-1453
nucleate cell1.24e-1355
intermediate monocyte2.78e-129
CD14-positive, CD16-positive monocyte2.78e-129
stem cell5.49e-12441
multi fate stem cell6.12e-12427
somatic stem cell9.72e-12433
granulocyte9.98e-098
lymphocyte of B lineage1.31e-0824
pro-B cell1.31e-0824
CD4-positive, alpha-beta T cell9.48e-086
B cell2.35e-0714
Uber Anatomy
Ontology termp-valuen
bone marrow5.39e-2976
bone element3.81e-2882
hematopoietic system1.37e-2698
blood island1.37e-2698
skeletal element4.80e-2490
immune system1.27e-2293
hemolymphoid system2.42e-22108
skeletal system7.82e-21100
connective tissue1.39e-16371
musculoskeletal system4.28e-08167
lateral plate mesoderm1.77e-07203


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)
MA0003.11.04263
MA0004.10.558729
MA0006.11.01439
MA0007.12.2901
MA0009.11.03681
MA0014.12.03395
MA0017.10.432438
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
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.808182
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.10.737586
MA0061.11.24837
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.11.72313
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.959858
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.12.61648
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
MA0131.11.84113
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.718193
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.21.47843
MA0138.21.80506
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.680553
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.11.39622
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.24.76174
MA0102.21.58513
MA0258.10.788656
MA0259.10.893594
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
BCL3#602211.51570093457940.01162725346801640.0424742471124925
E2F1#186954.089491012399440.001749817597761990.0107562801702569
E2F6#187654.180963109747820.001573598759586970.00997300084061553
NFKB1#479043.658708949462560.01207927289015230.0438219807341467
POLR2A#543062.147453176558070.01019570676818780.0379956973831496
SIN3A#2594254.507403939012610.001096110061208640.0076583247713787
TAF1#687263.343046285745290.0007162474284635620.00572685386474552
TBP#690853.088975572580320.006645448275786930.0282821504676003
ZNF263#1012745.481227758007120.002675609380607230.0147421771617641



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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