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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:37, 17 September 2013


Full id: C1077_thymus_CD8_Natural_blood_NK_Peripheral_acute



Phase1 CAGE Peaks

Hg19::chr2:87014966..87014973,-p@chr2:87014966..87014973
-
Hg19::chr2:87016482..87016502,-p@chr2:87016482..87016502
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Hg19::chr2:87017652..87017670,-p@chr2:87017652..87017670
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Hg19::chr2:87017971..87017982,-p4@CD8A
Hg19::chr2:87017985..87018050,-p1@CD8A
Hg19::chr2:87018060..87018074,-p2@CD8A
Hg19::chr2:87018470..87018477,-p7@CD8A
Hg19::chr2:87088995..87089018,-p1@CD8B


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

p.valueFDRnGenesnPathwayName
2.25318768070372e-050.002852535603770912136Cell adhesion molecules (CAMs) (KEGG):04514
7.37072179210596e-060.00198248117124819278Antigen processing and presentation (KEGG):04612
9.39564536136585e-060.00198248117124819288Hematopoietic cell lineage (KEGG):04640
1.41818283432528e-050.002244274335319762108T cell receptor signaling pathway (KEGG):04660
1.46039942267834e-060.000924432834555386235Primary immunodeficiency (KEGG):05340
0.0003198274735665560.03374179846127162511Signaling in Immune system (Reactome):REACT_6900



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:0042288MHC class I protein binding1.94443489268243e-06
GO:0042101T cell receptor complex1.94443489268243e-06
GO:0015026coreceptor activity2.00335716215766e-06
GO:0001772immunological synapse2.00335716215766e-06
GO:0042287MHC protein binding2.98146683544639e-06
GO:0042110T cell activation4.66762578026242e-05
GO:0043235receptor complex5.04627150719965e-05
GO:0046649lymphocyte activation8.79046607733516e-05
GO:0045321leukocyte activation0.000105470862360653
GO:0001775cell activation0.000117549927603074
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.000117549927603074
GO:0007167enzyme linked receptor protein signaling pathway0.000220221982163654
GO:0005102receptor binding0.00243469536960991
GO:0006955immune response0.00297248539808496
GO:0005887integral to plasma membrane0.00332669934433345
GO:0031226intrinsic to plasma membrane0.00332669934433345
GO:0002376immune system process0.00332669934433345
GO:0044459plasma membrane part0.00854199414041754
GO:0007166cell surface receptor linked signal transduction0.00917490442452626
GO:0043234protein complex0.0122393426537342
GO:0004872receptor activity0.0133734696582529
GO:0004871signal transducer activity0.017635448063124
GO:0060089molecular transducer activity0.017635448063124
GO:0005886plasma membrane0.0177636571829853
GO:0032991macromolecular complex0.0177636571829853
GO:0007165signal transduction0.0299540671128367
GO:0019882antigen processing and presentation0.0305786064897416
GO:0007154cell communication0.0325209261041257
GO:0016021integral to membrane0.0444991702929945
GO:0031224intrinsic to membrane0.0444991702929945



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
CD8-positive, alpha-beta T cell2.49e-3211
mature alpha-beta T cell5.12e-2218
alpha-beta T cell5.12e-2218
immature T cell5.12e-2218
mature T cell5.12e-2218
immature alpha-beta T cell5.12e-2218
T cell1.49e-2025
pro-T cell1.49e-2025
leukocyte8.18e-13136
lymphoid lineage restricted progenitor cell2.17e-1252
lymphocyte4.51e-1253
common lymphoid progenitor4.51e-1253
nongranular leukocyte6.05e-12115
nucleate cell1.80e-1155
natural killer cell1.38e-093
pro-NK cell1.38e-093
single nucleate cell3.21e-093
mononuclear cell3.21e-093
basophil6.57e-093
hematopoietic stem cell7.15e-09168
angioblastic mesenchymal cell7.15e-09168
hematopoietic lineage restricted progenitor cell2.67e-08120
hematopoietic cell4.89e-08177
hematopoietic oligopotent progenitor cell2.93e-07161
hematopoietic multipotent progenitor cell2.93e-07161
Uber Anatomy
Ontology termp-valuen
blood3.20e-2515
haemolymphatic fluid3.20e-2515
organism substance3.20e-2515
adult organism7.61e-21114
hemolymphoid system1.60e-11108
hematopoietic system4.95e-1198
blood island4.95e-1198
hemopoietic organ2.76e-107
immune organ2.76e-107
thymus2.58e-074
hemolymphoid system gland2.58e-074
thymic region2.58e-074
pharyngeal gland2.58e-074
thymus primordium2.58e-074
neck5.61e-0710
chordate pharynx7.55e-0710
pharyngeal region of foregut7.55e-0710


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)
MA0003.11.66566
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.11.03236
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.11.64271
MA0056.10
MA0057.10.632427
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.12.19892
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.441522
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.11.40058
MA0101.10.30624
MA0103.10.291333
MA0105.10.279181
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.913661
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.470675
MA0140.10.516266
MA0141.10.944441
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.830366
MA0146.10.934908
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.164269
MA0138.21.57302
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.21.21228
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.764865
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.0752715
MA0163.15.66754
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.481761
MA0102.21.46209
MA0258.10.603127
MA0259.10.25092
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

No analysis results for this cluster

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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