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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:30, 17 September 2013


Full id: C762_splenic_migratory_b_B_cord_CD14_mycosis



Phase1 CAGE Peaks

Hg19::chr17:38710881..38710891,-p@chr17:38710881..38710891
-
Hg19::chr17:38710907..38710919,-p@chr17:38710907..38710919
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Hg19::chr17:38711015..38711026,-p@chr17:38711015..38711026
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Hg19::chr17:38711096..38711107,-p@chr17:38711096..38711107
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Hg19::chr17:38711280..38711293,-p@chr17:38711280..38711293
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Hg19::chr17:38711427..38711449,-p@chr17:38711427..38711449
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Hg19::chr17:38711462..38711487,-p@chr17:38711462..38711487
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Hg19::chr17:38711642..38711651,-p@chr17:38711642..38711651
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Hg19::chr17:38711909..38711920,-p@chr17:38711909..38711920
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Hg19::chr17:38721717..38721730,-p1@CCR7
Hg19::chr5:68728816..68728820,+p@chr5:68728816..68728820
+


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
nongranular leukocyte9.83e-33115
leukocyte1.20e-32136
lymphocyte9.58e-2953
common lymphoid progenitor9.58e-2953
hematopoietic cell1.40e-27177
nucleate cell2.02e-2755
lymphoid lineage restricted progenitor cell3.44e-2752
hematopoietic lineage restricted progenitor cell3.66e-26120
hematopoietic stem cell2.76e-25168
angioblastic mesenchymal cell2.76e-25168
hematopoietic oligopotent progenitor cell6.10e-23161
hematopoietic multipotent progenitor cell6.10e-23161
T cell2.99e-1725
pro-T cell2.99e-1725
circulating cell7.02e-166
mature alpha-beta T cell3.50e-1518
alpha-beta T cell3.50e-1518
immature T cell3.50e-1518
mature T cell3.50e-1518
immature alpha-beta T cell3.50e-1518
CD8-positive, alpha-beta T cell1.49e-1011
Langerhans cell1.02e-095
classical monocyte1.90e-0942
CD14-positive, CD16-negative classical monocyte1.90e-0942
lymphocyte of B lineage2.51e-0924
pro-B cell2.51e-0924
single nucleate cell3.58e-083
mononuclear cell3.58e-083
defensive cell7.42e-0848
phagocyte7.42e-0848
CD4-positive, alpha-beta T cell2.70e-076
Uber Anatomy
Ontology termp-valuen
hemolymphoid system6.42e-15108
hematopoietic system1.14e-1498
blood island1.14e-1498
hemopoietic organ3.11e-127
immune organ3.11e-127
blood4.09e-1015
haemolymphatic fluid4.09e-1015
organism substance4.09e-1015
immune system8.11e-0993
spleen3.49e-083
gastrointestinal system mesentery3.49e-083
stomach region3.49e-083
mesentery3.49e-083
gastrointestinal system serosa3.49e-083
mesentery of stomach3.49e-083
gut mesentery3.49e-083
dorsal mesentery3.49e-083
dorsal mesogastrium3.49e-083
peritoneal cavity3.49e-083
spleen primordium3.49e-083
Disease
Ontology termp-valuen
lymphoma9.85e-0910


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)
MA0003.10.000970254
MA0004.10.349539
MA0006.10.605586
MA0007.10.332734
MA0009.10.79061
MA0014.10.00227771
MA0017.10.24363
MA0019.11.21992
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.11.68484
MA0030.10.696006
MA0031.10.633489
MA0038.11.12886
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.11.57917
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.136684
MA0056.10
MA0057.10.397382
MA0058.10.265212
MA0059.10.729981
MA0060.10.119532
MA0061.10.330174
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.556338
MA0069.10.776171
MA0070.10.765217
MA0071.11.05086
MA0072.11.79596
MA0073.13.85623e-06
MA0074.10.439193
MA0076.10.764079
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.467716
MA0089.10
MA0090.10.291627
MA0091.10.927876
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.587485
MA0105.10.0403209
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.11.3572
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.637178
MA0140.10.405425
MA0141.10.726533
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.277793
MA0146.10.184736
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.21.84093
MA0039.20.0194173
MA0138.20.534556
MA0002.21.19327
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.20.260758
MA0065.20.11899
MA0150.10.781086
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.353037
MA0155.10.0230394
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.11.0031
MA0161.10
MA0162.10.00470038
MA0163.10.232847
MA0164.10.509774
MA0080.20.611699
MA0018.21.21486
MA0099.21.05945
MA0079.22.06734e-05
MA0102.21.32663
MA0258.10.831523
MA0259.10.168926
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#1066483.898368271327290.0001406611760594710.00183447959121817
POLR2A#5430112.147453176558070.0002231983422387430.00248566982992878
STAT2#6773211.86614021571650.011775288421530.0429069620911373



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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