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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:29, 17 September 2013


Full id: C739_granulocyte_CD34_CD19_CD14CD16_CD4_Mesothelial_Dendritic



Phase1 CAGE Peaks

Hg19::chr11:5248320..5248322,+p@chr11:5248320..5248322
+
Hg19::chr15:39872100..39872101,-p@chr15:39872100..39872101
-
Hg19::chr17:37864788..37864790,-p@chr17:37864788..37864790
-
Hg19::chr17:7145967..7145970,+p@chr17:7145967..7145970
+
Hg19::chr19:39786962..39786965,+p2@IL29
Hg19::chr19:39786984..39786986,-p@chr19:39786984..39786986
-
Hg19::chr1:36786251..36786257,+p12@SH3D21
Hg19::chr20:62243927..62243929,+p@chr20:62243927..62243929
+
Hg19::chr21:34143971..34143983,-p8@GCFC1
Hg19::chr6:111580680..111580691,+p3@KIAA1919
Hg19::chr8:104151242..104151262,+p@chr8:104151242..104151262
+


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:0032003interleukin-28 receptor binding0.00426815806625265
GO:0045345positive regulation of MHC class I biosynthetic process0.00426815806625265
GO:0045341MHC class I biosynthetic process0.00426815806625265
GO:0045343regulation of MHC class I biosynthetic process0.00426815806625265
GO:0032002interleukin-28 receptor complex0.00512171429365841
GO:0046427positive regulation of JAK-STAT cascade0.00853568791713221
GO:0042531positive regulation of tyrosine phosphorylation of STAT protein0.00853568791713221
GO:0042509regulation of tyrosine phosphorylation of STAT protein0.0128014587649671
GO:0046425regulation of JAK-STAT cascade0.0128014587649671
GO:0051607defense response to virus0.0128014587649671
GO:0050731positive regulation of peptidyl-tyrosine phosphorylation0.0128014587649671
GO:0007260tyrosine phosphorylation of STAT protein0.0128014587649671
GO:0042327positive regulation of phosphorylation0.013273632419546
GO:0045937positive regulation of phosphate metabolic process0.013273632419546
GO:0001934positive regulation of protein amino acid phosphorylation0.013273632419546
GO:0033240positive regulation of amine metabolic process0.013273632419546
GO:0045764positive regulation of amino acid metabolic process0.013273632419546
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.013273632419546
GO:0007259JAK-STAT cascade0.0163506766880092
GO:0018108peptidyl-tyrosine phosphorylation0.0163506766880092
GO:0018212peptidyl-tyrosine modification0.0163506766880092
GO:0001932regulation of protein amino acid phosphorylation0.0163506766880092
GO:0033238regulation of amine metabolic process0.0163506766880092
GO:0006521regulation of amino acid metabolic process0.0163506766880092
GO:0045727positive regulation of translation0.0180834056716837
GO:0031328positive regulation of cellular biosynthetic process0.0192562602658128
GO:0042325regulation of phosphorylation0.0192562602658128
GO:0016324apical plasma membrane0.0192562602658128
GO:0051174regulation of phosphorus metabolic process0.0192562602658128
GO:0019220regulation of phosphate metabolic process0.0192562602658128
GO:0009891positive regulation of biosynthetic process0.0192562602658128
GO:0044459plasma membrane part0.0198232630492858
GO:0050778positive regulation of immune response0.0198232630492858
GO:0051247positive regulation of protein metabolic process0.0198232630492858
GO:0045177apical part of cell0.0198232630492858
GO:0002684positive regulation of immune system process0.0198232630492858
GO:0005351sugar:hydrogen ion symporter activity0.0198232630492858
GO:0051119sugar transmembrane transporter activity0.0198232630492858
GO:0031402sodium ion binding0.0198232630492858
GO:0015144carbohydrate transmembrane transporter activity0.0198232630492858
GO:0050776regulation of immune response0.0198232630492858
GO:0009615response to virus0.0198232630492858
GO:0002682regulation of immune system process0.0198232630492858
GO:0051240positive regulation of multicellular organismal process0.020127892237198
GO:0043235receptor complex0.020127892237198
GO:0002252immune effector process0.020127892237198
GO:0008643carbohydrate transport0.020127892237198
GO:0018193peptidyl-amino acid modification0.0214809399458696
GO:0009967positive regulation of signal transduction0.0265949721698051
GO:0006814sodium ion transport0.0294613158369408
GO:0006417regulation of translation0.0307151888842789
GO:0031326regulation of cellular biosynthetic process0.0325731024021994
GO:0051707response to other organism0.0330792660137437
GO:0005886plasma membrane0.0335730676928623
GO:0009889regulation of biosynthetic process0.0335730676928623
GO:0031420alkali metal ion binding0.0335853857639441
GO:0008285negative regulation of cell proliferation0.0335853857639441
GO:0015293symporter activity0.0354912267981477
GO:0051239regulation of multicellular organismal process0.0395320354538901
GO:0045941positive regulation of transcription0.0395320354538901
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.039622163689615
GO:0009607response to biotic stimulus0.039622163689615
GO:0005125cytokine activity0.041813676195433
GO:0051704multi-organism process0.0441991330548567
GO:0015291secondary active transmembrane transporter activity0.0469561865029264
GO:0031325positive regulation of cellular metabolic process0.0469561865029264
GO:0007243protein kinase cascade0.0476415885686142
GO:0009893positive regulation of metabolic process0.0488027856147575



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><br><br>

Cell Type
Ontology termp-valuen
plasmacytoid dendritic cell1.79e-173
CD34-positive, CD38-negative hematopoietic stem cell5.15e-141
CD4-positive, alpha-beta thymocyte1.10e-131
naive thymus-derived CD4-positive, alpha-beta T cell1.10e-131
mature CD4 single-positive thymocyte1.10e-131
resting double-positive thymocyte1.10e-131
double-positive blast1.10e-131
CD69-positive double-positive thymocyte1.10e-131
CD69-positive, CD4-positive single-positive thymocyte1.10e-131
CD4-positive, CD8-intermediate double-positive thymocyte1.10e-131
CD24-positive, CD4 single-positive thymocyte1.10e-131
B cell1.09e-0814
hematopoietic stem cell1.44e-07168
angioblastic mesenchymal cell1.44e-07168
thymocyte1.75e-072
double negative thymocyte1.75e-072
double-positive, alpha-beta thymocyte1.75e-072
DN4 thymocyte1.75e-072
DN1 thymic pro-T cell1.75e-072
DN2 thymocyte1.75e-072
DN3 thymocyte1.75e-072
immature single positive thymocyte1.75e-072
early T lineage precursor1.75e-072
hematopoietic cell4.13e-07177


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)
MA0003.10.0768054
MA0004.10.349539
MA0006.10.605586
MA0007.10.885261
MA0009.10.79061
MA0014.10.21986
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.185335
MA0050.10.897608
MA0051.10.439895
MA0052.10.716602
MA0055.10.279754
MA0056.10
MA0057.10.176435
MA0058.10.732537
MA0059.10.729981
MA0060.10.119532
MA0061.11.12119
MA0063.10
MA0066.11.12972
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.00132306
MA0074.10.439193
MA0076.10.764079
MA0077.10.753278
MA0078.10.533387
MA0081.11.34305
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.10094
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.61153
MA0095.10
MA0098.10
MA0100.11.15683
MA0101.10.216017
MA0103.10.587485
MA0105.10.645738
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.11.49522
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
MA0139.10.0922451
MA0140.10.405425
MA0141.10.726533
MA0142.10.602852
MA0143.10.498176
MA0144.10.438224
MA0145.10.515404
MA0146.10.315774
MA0147.10.488526
MA0148.10.372124
MA0149.10.396509
MA0062.20.659456
MA0035.20.404774
MA0039.20.267159
MA0138.20.534556
MA0002.20.725804
MA0137.20.229531
MA0104.20.378829
MA0047.20.47109
MA0112.20.784016
MA0065.20.28513
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.153348
MA0155.10.099499
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.489747
MA0160.10.386031
MA0161.10
MA0162.10.324348
MA0163.10.0158063
MA0164.10.509774
MA0080.20.611699
MA0018.20.483823
MA0099.20.411824
MA0079.20.00352009
MA0102.21.32663
MA0258.10.831523
MA0259.10.973858
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
STAT1#677235.647251135599780.01386896002832930.0487188562913687
STAT2#6773211.86614021571650.011775288421530.0429054651451759
XRCC4#75181390.7547568710360.002556244126181940.0141456885653746



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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