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

Latest revision as of 11:29, 17 September 2013


Full id: C726_chronic_CD4_Hodgkin_CD8_thymus_CD19_blood



Phase1 CAGE Peaks

Hg19::chr10:6622629..6622638,+p4@uc001ijl.2
Hg19::chr10:6622667..6622678,+p5@uc001ijl.2
Hg19::chr11:118211212..118211232,-p@chr11:118211212..118211232
-
Hg19::chr11:6423982..6423997,-p9@APBB1
Hg19::chr15:22448832..22448885,-p1@AJ004954
Hg19::chr1:117307142..117307156,+p3@CD2
Hg19::chr1:117307157..117307178,+p2@CD2
Hg19::chr1:117311220..117311234,+p@chr1:117311220..117311234
+
Hg19::chr2:99388276..99388311,-p3@ENST00000448595
Hg19::chr2:99388349..99388378,-p1@ENST00000448595
Hg19::chr9:35649814..35649823,-p@chr9:35649814..35649823
-


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:0030887positive regulation of myeloid dendritic cell activation0.00239899918896269
GO:0050760negative regulation of thymidylate synthase biosynthetic process0.00239899918896269
GO:0050758regulation of thymidylate synthase biosynthetic process0.00239899918896269
GO:0050757thymidylate synthase biosynthetic process0.00239899918896269
GO:0051665lipid raft localization0.00239899918896269
GO:0031580lipid raft distribution0.00239899918896269
GO:0001766lipid raft polarization0.00239899918896269
GO:0030885regulation of myeloid dendritic cell activation0.00239899918896269
GO:0001773myeloid dendritic cell activation0.00383828571022355
GO:0031579lipid raft organization and biogenesis0.00383828571022355
GO:0045749negative regulation of S phase of mitotic cell cycle0.00610609398962248
GO:0045580regulation of T cell differentiation0.0073369270873641
GO:0001540beta-amyloid binding0.0073369270873641
GO:0007090regulation of S phase of mitotic cell cycle0.0073369270873641
GO:0045930negative regulation of progression through mitotic cell cycle0.0073369270873641
GO:0007009plasma membrane organization and biogenesis0.0073369270873641
GO:0051668localization within membrane0.0073369270873641
GO:0033261regulation of progression through S phase0.00784942111105822
GO:0045619regulation of lymphocyte differentiation0.00784942111105822
GO:0000084S phase of mitotic cell cycle0.00784942111105822
GO:0030101natural killer cell activation0.00784942111105822
GO:0030426growth cone0.00784942111105822
GO:0030427site of polarized growth0.00792514425191407
GO:0051320S phase0.00839414904394305
GO:0048468cell development0.00870786176931244
GO:0002274myeloid leukocyte activation0.0099614067426714
GO:0007346regulation of progression through mitotic cell cycle0.0113680113202635
GO:0048731system development0.0126841943224681
GO:0030027lamellipodium0.0126841943224681
GO:0030217T cell differentiation0.0126841943224681
GO:0017148negative regulation of translation0.0126841943224681
GO:0031327negative regulation of cellular biosynthetic process0.0134858298228399
GO:0048869cellular developmental process0.0136017999257637
GO:0030154cell differentiation0.0136017999257637
GO:0009890negative regulation of biosynthetic process0.0139726535835333
GO:0030308negative regulation of cell growth0.0139942492563816
GO:0045792negative regulation of cell size0.0139942492563816
GO:0050863regulation of T cell activation0.0145514290056884
GO:0048856anatomical structure development0.0145514290056884
GO:0045926negative regulation of growth0.0146211869705408
GO:0030098lymphocyte differentiation0.0149654475969592
GO:0031252leading edge0.0164333313353733
GO:0051249regulation of lymphocyte activation0.01694189346195
GO:0007275multicellular organismal development0.0169587749440453
GO:0050865regulation of cell activation0.017039964487941
GO:0051329interphase of mitotic cell cycle0.0177100711960359
GO:0002521leukocyte differentiation0.0179691892931388
GO:0051325interphase0.0179691892931388
GO:0042110T cell activation0.0191648754036795
GO:0007050cell cycle arrest0.0193556682424319
GO:0051248negative regulation of protein metabolic process0.019538929159613
GO:0007409axonogenesis0.0210026976150678
GO:0048667neuron morphogenesis during differentiation0.0212874009302865
GO:0048812neurite morphogenesis0.0212874009302865
GO:0000904cellular morphogenesis during differentiation0.0219434337308529
GO:0031175neurite development0.0230879213432029
GO:0048666neuron development0.0254244349158173
GO:0046649lymphocyte activation0.0254244349158173
GO:0016043cellular component organization and biogenesis0.0254244349158173
GO:0030097hemopoiesis0.0254244349158173
GO:0001558regulation of cell growth0.0254244349158173
GO:0032502developmental process0.0255122121187149
GO:0048534hemopoietic or lymphoid organ development0.0262752118608913
GO:0045321leukocyte activation0.0262752118608913
GO:0002520immune system development0.0262752118608913
GO:0006417regulation of translation0.0262752118608913
GO:0031326regulation of cellular biosynthetic process0.0262752118608913
GO:0016049cell growth0.0262752118608913
GO:0040008regulation of growth0.0262752118608913
GO:0032990cell part morphogenesis0.0262752118608913
GO:0048858cell projection morphogenesis0.0262752118608913
GO:0030030cell projection organization and biogenesis0.0262752118608913
GO:0008361regulation of cell size0.0262752118608913
GO:0001775cell activation0.0262752118608913
GO:0030182neuron differentiation0.0262752118608913
GO:0006917induction of apoptosis0.0262752118608913
GO:0012502induction of programmed cell death0.0262752118608913
GO:0032501multicellular organismal process0.0262752118608913
GO:0009889regulation of biosynthetic process0.0262752118608913
GO:0045786negative regulation of progression through cell cycle0.0269001568217935
GO:0048699generation of neurons0.0285682467560399
GO:0043065positive regulation of apoptosis0.0297161269138546
GO:0043068positive regulation of programmed cell death0.0297161269138546
GO:0022008neurogenesis0.0298158318010825
GO:0051239regulation of multicellular organismal process0.0311450839206244
GO:0016044membrane organization and biogenesis0.0315575748587551
GO:0042995cell projection0.0343654970695894
GO:0000278mitotic cell cycle0.0353792794685426
GO:0016337cell-cell adhesion0.0372236214630119
GO:0000074regulation of progression through cell cycle0.0374431864112437
GO:0051726regulation of cell cycle0.0376578140057725
GO:0022403cell cycle phase0.0382803873763502
GO:0031324negative regulation of cellular metabolic process0.0390933314854237
GO:0007165signal transduction0.0397200677172096
GO:0051246regulation of protein metabolic process0.0423629181842233
GO:0008134transcription factor binding0.0428569954657122
GO:0009892negative regulation of metabolic process0.0428569954657122
GO:0007154cell communication0.0445454702098529
GO:0000902cell morphogenesis0.0454903912728169
GO:0032989cellular structure morphogenesis0.0454903912728169
GO:0050794regulation of cellular process0.0454903912728169



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
T cell2.34e-5425
pro-T cell2.34e-5425
mature alpha-beta T cell7.64e-5218
alpha-beta T cell7.64e-5218
immature T cell7.64e-5218
mature T cell7.64e-5218
immature alpha-beta T cell7.64e-5218
lymphoid lineage restricted progenitor cell1.83e-3552
lymphocyte1.18e-3453
common lymphoid progenitor1.18e-3453
nucleate cell4.00e-3355
CD8-positive, alpha-beta T cell1.72e-3211
nongranular leukocyte1.86e-19115
CD4-positive, alpha-beta T cell2.44e-186
leukocyte1.79e-16136
hematopoietic lineage restricted progenitor cell1.79e-14120
hematopoietic stem cell9.39e-12168
angioblastic mesenchymal cell9.39e-12168
hematopoietic cell9.59e-11177
naive T cell3.51e-103
natural killer cell2.15e-093
pro-NK cell2.15e-093
single nucleate cell2.72e-093
mononuclear cell2.72e-093
hematopoietic oligopotent progenitor cell5.81e-09161
hematopoietic multipotent progenitor cell5.81e-09161
regulatory T cell2.05e-072
CD4-positive, CD25-positive, alpha-beta regulatory T cell2.05e-072
naive regulatory T cell2.05e-072
thymocyte5.85e-072
double negative thymocyte5.85e-072
double-positive, alpha-beta thymocyte5.85e-072
DN4 thymocyte5.85e-072
DN1 thymic pro-T cell5.85e-072
DN2 thymocyte5.85e-072
DN3 thymocyte5.85e-072
immature single positive thymocyte5.85e-072
early T lineage precursor5.85e-072
Uber Anatomy
Ontology termp-valuen
hemopoietic organ8.89e-157
immune organ8.89e-157
blood2.34e-1415
haemolymphatic fluid2.34e-1415
organism substance2.34e-1415
thymus1.08e-124
hemolymphoid system gland1.08e-124
thymic region1.08e-124
pharyngeal gland1.08e-124
thymus primordium1.08e-124
pharyngeal epithelium1.84e-086
chordate pharynx2.26e-0710
pharyngeal region of foregut2.26e-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)
MA0003.10.0768054
MA0004.10.349539
MA0006.10.210781
MA0007.10.885261
MA0009.10.79061
MA0014.10.559573
MA0017.11.26613
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.637069
MA0029.10.707146
MA0030.10.696006
MA0031.11.53137
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.729247
MA0050.10.897608
MA0051.10.439895
MA0052.10.716602
MA0055.10.279754
MA0056.10
MA0057.10.176435
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.11.12119
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.00428338
MA0074.10.439193
MA0076.10.278993
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
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.617985
MA0103.10.203171
MA0105.10.15707
MA0106.10.482519
MA0107.10.475157
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.11.45594
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.11.57257
MA0140.11.04551
MA0141.10.2626
MA0142.11.46715
MA0143.11.24556
MA0144.10.142196
MA0145.10.115359
MA0146.10.951488
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.659456
MA0035.21.04409
MA0039.20.00136845
MA0138.20.534556
MA0002.20.358551
MA0137.20.229531
MA0104.20.118985
MA0047.21.18756
MA0112.20.260758
MA0065.20.839576
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.153348
MA0155.10.74825
MA0156.10.654264
MA0157.11.41182
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.00470038
MA0163.10.387319
MA0164.10.509774
MA0080.20.611699
MA0018.20.483823
MA0099.20.411824
MA0079.20.00715613
MA0102.21.32663
MA0258.10.420151
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
EBF1#187954.048394021167730.004592383252421630.0217024395701205



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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