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

Latest revision as of 11:17, 17 September 2013


Full id: C300_CD4_CD8_NK_Natural_blood_mycosis_Basophils



Phase1 CAGE Peaks

Hg19::chr14:22362614..22362619,+p1@TRAV8-4
Hg19::chr14:22446777..22446791,+p2@uc010tml.1
p2@uc010tmm.1
Hg19::chr14:91708304..91708315,+p@chr14:91708304..91708315
+
Hg19::chr14:91708318..91708330,+p@chr14:91708318..91708330
+
Hg19::chr14:94442986..94442992,-p15@ASB2
Hg19::chr18:67624010..67624041,-p5@CD226
Hg19::chr19:17295496..17295508,+p@chr19:17295496..17295508
+
Hg19::chr1:150082476..150082490,+p@chr1:150082476..150082490
+
Hg19::chr22:39147814..39147833,-p11@SUN2
Hg19::chr2:182249921..182249925,+p@chr2:182249921..182249925
+
Hg19::chr2:191931233..191931243,-p@chr2:191931233..191931243
-
Hg19::chr2:197041193..197041212,-p5@STK17B
Hg19::chr2:39347524..39347552,-p4@SOS1
Hg19::chr2:39347770..39347791,-p5@SOS1
Hg19::chr2:39348137..39348212,-p1@SOS1
Hg19::chr2:39348418..39348431,-p17@SOS1
Hg19::chr2:39348469..39348498,-p9@SOS1
Hg19::chr2:39351689..39351715,+p@chr2:39351689..39351715
+
Hg19::chr2:7865859..7865862,+p3@ENST00000417930
Hg19::chr2:7865873..7865921,+p1@ENST00000417930
Hg19::chr2:7865923..7865941,+p2@ENST00000417930
Hg19::chr3:45984947..45984966,+p1@CXCR6
Hg19::chr3:46395344..46395359,+p2@CCR2
Hg19::chr3:46395363..46395374,+p7@CCR2
Hg19::chr3:4867715..4867729,-p@chr3:4867715..4867729
-
Hg19::chr3:51715738..51715765,+p2@TEX264
Hg19::chr4:6692260..6692274,-p2@ENST00000499502
Hg19::chr4:6692355..6692360,-p3@ENST00000499502
Hg19::chr5:54398463..54398480,+p1@GZMA
Hg19::chr6:128201709..128201716,-p@chr6:128201709..128201716
-
Hg19::chr6:149555824..149555843,-p@chr6:149555824..149555843
-
Hg19::chrX:135721685..135721705,+p1@LOC100128420
Hg19::chrX:135721762..135721773,+p4@ENST00000429841
Hg19::chrX:135721794..135721808,+p3@ENST00000429841
Hg19::chrX:135721811..135721833,+p1@ENST00000429841
Hg19::chrX:135721840..135721857,+p2@ENST00000429841
Hg19::chrX:135721874..135721887,+p1@ENST00000427517
p1@uc004ezz.2
Hg19::chrX:135730297..135730350,+p1@CD40LG
Hg19::chrX:135730373..135730399,+p2@CD40LG
Hg19::chrX:135741632..135741643,+p@chrX:135741632..135741643
+
Hg19::chrX:135742035..135742051,+p@chrX:135742035..135742051
+
Hg19::chrX:135742088..135742115,+p@chrX:135742088..135742115
+


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
0.0001635625119434310.02588376751504793265Cytokine-cytokine receptor interaction (KEGG):04060
6.01405003919819e-050.01268964558270823189Chemokine signaling pathway (KEGG):04062
4.48189730095749e-050.01268964558270824511Signaling in Immune system (Reactome):REACT_6900
2.34678751347395e-050.01268964558270824433IL-2 up reg. targets (Netpath):NetPath_14



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:0019957C-C chemokine binding0.00203275243585207
GO:0016493C-C chemokine receptor activity0.00203275243585207
GO:0004950chemokine receptor activity0.00203275243585207
GO:0001637G-protein chemoattractant receptor activity0.00203275243585207
GO:0019956chemokine binding0.00203275243585207
GO:0007165signal transduction0.00203275243585207
GO:0007242intracellular signaling cascade0.00236279697749897
GO:0007154cell communication0.00257076988205919
GO:0044459plasma membrane part0.00378351305242138
GO:0005887integral to plasma membrane0.00438007771105616
GO:0031226intrinsic to plasma membrane0.00438007771105616
GO:0031727CCR2 chemokine receptor binding0.00438007771105616
GO:0048020CCR chemokine receptor binding0.00438007771105616
GO:0004277granzyme A activity0.00438007771105616
GO:0005174CD40 receptor binding0.00438007771105616
GO:0019955cytokine binding0.00462889244648079
GO:0001816cytokine production0.00567214870023238
GO:0032735positive regulation of interleukin-12 production0.0072992699464958
GO:0001653peptide receptor activity0.00824820650737661
GO:0008528peptide receptor activity, G-protein coupled0.00824820650737661
GO:0006922cleavage of lamin0.00856769927397956
GO:0006923cleavage of cytoskeletal proteins during apoptosis0.00856769927397956
GO:0032655regulation of interleukin-12 production0.00856769927397956
GO:0006915apoptosis0.0120987350741618
GO:0012501programmed cell death0.0120987350741618
GO:0042277peptide binding0.0124533973568257
GO:0008219cell death0.0125502845118458
GO:0016265death0.0125502845118458
GO:0005886plasma membrane0.0130053297491197
GO:0032615interleukin-12 production0.0131324991110303
GO:0005625soluble fraction0.013179067182002
GO:0005515protein binding0.0151343927086091
GO:0006954inflammatory response0.0185092915895833
GO:0007159leukocyte adhesion0.0185092915895833
GO:0016494C-X-C chemokine receptor activity0.0185092915895833
GO:0002208somatic diversification of immunoglobulins during immune response0.0185092915895833
GO:0002381immunoglobulin production during immune response0.0185092915895833
GO:0002204somatic recombination of immunoglobulin genes during immune response0.0185092915895833
GO:0045190isotype switching0.0185092915895833
GO:0006955immune response0.0190092271228569
GO:0019958C-X-C chemokine binding0.0192047199434155
GO:0016447somatic recombination of immunoglobulin gene segments0.0197993162207085
GO:0048468cell development0.0197993162207085
GO:0031280negative regulation of cyclase activity0.0197993162207085
GO:0016444somatic cell DNA recombination0.0197993162207085
GO:0007194negative regulation of adenylate cyclase activity0.0197993162207085
GO:0051350negative regulation of lyase activity0.0197993162207085
GO:0016445somatic diversification of immunoglobulins0.0197993162207085
GO:0002562somatic diversification of immune receptors via germline recombination within a single locus0.0197993162207085
GO:0007243protein kinase cascade0.0197993162207085
GO:0015026coreceptor activity0.0197993162207085
GO:0002200somatic diversification of immune receptors0.0197993162207085
GO:0019835cytolysis0.0197993162207085
GO:0001772immunological synapse0.0206447731653015
GO:0002376immune system process0.020706251242198
GO:0002377immunoglobulin production0.020706251242198
GO:0042100B cell proliferation0.020706251242198
GO:0009611response to wounding0.0224701169761612
GO:0006921cell structure disassembly during apoptosis0.0233301615954918
GO:0001819positive regulation of cytokine production0.0251202993534965
GO:0005100Rho GTPase activator activity0.0257797388481279
GO:0030168platelet activation0.026417657728311
GO:0002440production of molecular mediator of immune response0.0280715875138972
GO:0019079viral genome replication0.0296728701447912
GO:0042981regulation of apoptosis0.0356996152922203
GO:0043067regulation of programmed cell death0.0357711508412229
GO:0006952defense response0.0357711508412229
GO:0048869cellular developmental process0.0357711508412229
GO:0030154cell differentiation0.0357711508412229
GO:0005164tumor necrosis factor receptor binding0.0359283039721178
GO:0007259JAK-STAT cascade0.0359283039721178
GO:0001817regulation of cytokine production0.0361337348780551
GO:0045761regulation of adenylate cyclase activity0.0361337348780551
GO:0032813tumor necrosis factor receptor superfamily binding0.0361337348780551
GO:0031279regulation of cyclase activity0.0361337348780551
GO:0051339regulation of lyase activity0.0361337348780551
GO:0019221cytokine and chemokine mediated signaling pathway0.0363786717589302
GO:0009605response to external stimulus0.0363786717589302
GO:0022411cellular component disassembly0.0405217762126783
GO:0019058viral infectious cycle0.0408270885386266
GO:0016064immunoglobulin mediated immune response0.0411246731931978
GO:0019724B cell mediated immunity0.0412013747883468
GO:0032943mononuclear cell proliferation0.0412013747883468
GO:0046651lymphocyte proliferation0.0412013747883468
GO:0022415viral reproductive process0.0437690085605704
GO:0042113B cell activation0.0462740844094532



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
mature alpha-beta T cell3.66e-5418
alpha-beta T cell3.66e-5418
immature T cell3.66e-5418
mature T cell3.66e-5418
immature alpha-beta T cell3.66e-5418
T cell7.29e-4225
pro-T cell7.29e-4225
CD8-positive, alpha-beta T cell4.99e-3411
lymphoid lineage restricted progenitor cell4.75e-2452
lymphocyte1.75e-2353
common lymphoid progenitor1.75e-2353
nucleate cell2.06e-2255
CD4-positive, alpha-beta T cell1.05e-186
nongranular leukocyte4.29e-15115
leukocyte9.71e-13136
hematopoietic lineage restricted progenitor cell8.88e-11120
naive T cell3.49e-103
natural killer cell6.10e-103
pro-NK cell6.10e-103
single nucleate cell8.05e-103
mononuclear cell8.05e-103
hematopoietic stem cell5.88e-09168
angioblastic mesenchymal cell5.88e-09168
hematopoietic cell3.75e-08177
thymocyte1.13e-072
double negative thymocyte1.13e-072
double-positive, alpha-beta thymocyte1.13e-072
DN4 thymocyte1.13e-072
DN1 thymic pro-T cell1.13e-072
DN2 thymocyte1.13e-072
DN3 thymocyte1.13e-072
immature single positive thymocyte1.13e-072
early T lineage precursor1.13e-072
hematopoietic oligopotent progenitor cell3.04e-07161
hematopoietic multipotent progenitor cell3.04e-07161
regulatory T cell4.02e-072
CD4-positive, CD25-positive, alpha-beta regulatory T cell4.02e-072
naive regulatory T cell4.02e-072
Uber Anatomy
Ontology termp-valuen
blood2.82e-2315
haemolymphatic fluid2.82e-2315
organism substance2.82e-2315
hemopoietic organ6.95e-157
immune organ6.95e-157
thymus1.44e-124
hemolymphoid system gland1.44e-124
thymic region1.44e-124
pharyngeal gland1.44e-124
thymus primordium1.44e-124
pharyngeal epithelium2.16e-086
hematopoietic system2.95e-0898
blood island2.95e-0898
hemolymphoid system6.07e-08108
chordate pharynx1.94e-0710
pharyngeal region of foregut1.94e-0710
neck2.61e-0710
pharynx9.88e-0711


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)
MA0003.10.00745649
MA0004.10.0477118
MA0006.10.151261
MA0007.11.94772
MA0009.10.309236
MA0014.10.00210299
MA0017.10.203459
MA0019.10.713554
MA0024.10.234026
MA0025.11.06411
MA0027.11.81465
MA0028.10.17175
MA0029.11.28007
MA0030.10.672868
MA0031.10.571644
MA0038.10.294316
MA0040.10.700752
MA0041.10.198966
MA0042.10.0434862
MA0043.10.833138
MA0046.10.301098
MA0048.10.210301
MA0050.10.381055
MA0051.10.0854137
MA0052.10.254136
MA0055.10.0684641
MA0056.10
MA0057.10.00336561
MA0058.10.0972791
MA0059.11.47391
MA0060.10.00188989
MA0061.10.0074676
MA0063.10
MA0066.10.0874771
MA0067.10.570397
MA0068.11.27583
MA0069.10.298233
MA0070.11.43734
MA0071.10.248466
MA0072.10.286664
MA0073.10.502261
MA0074.11.50408
MA0076.10.109351
MA0077.10.281032
MA0078.11.34277
MA0081.10.45252
MA0083.10.845316
MA0084.10.739331
MA0087.10.284873
MA0088.10.0310472
MA0089.10
MA0090.10.0292582
MA0091.10.182723
MA0092.10.614384
MA0093.10.057639
MA0095.10
MA0098.10
MA0100.10.0935814
MA0101.10.318901
MA0103.10.140019
MA0105.10.0022172
MA0106.10.106627
MA0107.10.175927
MA0108.20.566954
MA0109.10
MA0111.10.0326717
MA0113.10.114834
MA0114.10.494361
MA0115.10.50405
MA0116.10.181804
MA0117.10.337847
MA0119.10.214757
MA0122.10.357986
MA0124.10.468805
MA0125.10.399431
MA0130.10
MA0131.10.444261
MA0132.10
MA0133.10
MA0135.10.332279
MA0136.13.46004
MA0139.10.219459
MA0140.11.35002
MA0141.10.0217901
MA0142.10.176637
MA0143.10.114924
MA0144.12.79201
MA0145.10.0798025
MA0146.10.00945976
MA0147.10.0859124
MA0148.11.68086
MA0149.10.0660182
MA0062.20.0648737
MA0035.20.24463
MA0039.22.18142e-05
MA0138.20.135185
MA0002.20.465514
MA0137.21.63724
MA0104.20.0415431
MA0047.21.65119
MA0112.20.00216779
MA0065.20.0465065
MA0150.13.2049
MA0151.10
MA0152.10.918228
MA0153.10.385866
MA0154.10.472017
MA0155.10.0137096
MA0156.13.67919
MA0157.10.160178
MA0158.10
MA0159.10.0288354
MA0160.10.221938
MA0161.10
MA0162.10.001959
MA0163.10.0550107
MA0164.10.121237
MA0080.22.38435
MA0018.20.107308
MA0099.23.14275
MA0079.21.28116e-05
MA0102.20.773745
MA0258.10.00282645
MA0259.10.0938676
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
RXRA#625673.345769523188880.004404025343448630.0208670720825892



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

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