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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.507314523107256,0.408224900384208,0.399546206658198,0.144064671875115,0.247398438714038,0.209317792906133,0,0,0,0.142181656843797,0.267879027469464,0.200631895234306,0,0.343067067616665,0.409067668392705,0.160717855764157,0.21690115973835,0.0995340912392844,0.591950640554598,0.399933835234624,0.34496577392992,0.543186273210671,0.348986669269068,0.350020241648737,0.479121164717847,0.306348418993444,0.338936571693931,0.376391288041361,0.216293844171574,0,0.560551337204814,0.259765472565373,0.370761143316164,0.537651782554888,0.303617492015383,0.403876813852756,0.365376626635383,0.446408679939277,0.267746377672919,0.481652511202126,0.329351182440039,0.542985799592082,0.399239554639478,0.428176138987405,0.437355834505678,0.665805773168088,0.323217625098021,0.412008702850566,0.620014111989638,0.622117047291444,0.311392129055566,0.349397003731491,0.312016106298899,0.327375101464831,0.268352864591719,0.475550145930845,0.391166886134781,0.440903172569491,0.320619227153203,0.276349023213624,0.267983322146663,0.415237844311434,0.332338435410287,0.419648228777591,0.290936506658587,0.432590746050352,0.524908502418249,0.331795568716987,0,0,0.312502392473871,0.201432442864018,0.695891865856917,0.539981147109775,0.767037689711026,0.461041944431859,0.289342666169155,0.469566853250347,0.891873940077468,0.709650031707148,0.657490151408224,0.655181691937234,0.838357916024813,0.792557943593073,0.785157153870726,0.740900581894644,0.67828524643092,0.527962905465105,0.565305589486037,0.490058324208733,0.751716493145097,0.464802780451588,0.485971807789317,0.577861208011299,0.413773552501943,0.415275642600153,0.407508746977973,0.448227161611277,0.519008359335698,0.297024162867849,0.527342748963584,0.478290478090097,0.256820409353761,0.532367259302191,0.481090127086401,0,0.16787407288081,0,0,0,0,0,0,0,0,0.00907511092516647,0,0,0.0819445437133025,0.12206750241012,0.271992233335367,0.414220284635839,0.16937498165142,0.196451135708678,0,0,0,0,0,0.152135224370875,0.190397841472823,0,0,0,0,0,0,0,0,0,0.0371473953017556,0,0.0270049599589053,0,0,0,0.365076740692652,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.104741781954859,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.178878448616497,0,0,0,0,0,0,0.611748971600353,0,0,0,0,0.0917592878235724,0,0,0,0,0,0,0,0,0,0,0,0.112684970904787,0.336464001860819,0.340255542172246,0,0,0,0,0,0,0.173961836914205,0.294142649764829,0.21004665862461,0.235679859774857,0.244884114925612,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.345616359157155,0.484255970729509,0.86480870717144,0,0,0,0,0,0,0.390424046538658,0.321409124703051,0.554795650204648,0.446661800390021,0,0,0,0,0,0.739891986482216,1.3967730867025,0.744963129787065,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.209596525138408,0.60422592468244,0.396928803964221,0,0,0,0,0,0,0,0,0,0,0,0,0,0.126605887942362,0,0,0.255761024149889,0,0,0,0,0,0,0,0,0,0,0.0682206429897042,0,0,0,0,0,0,0,0,0,0,0,0,0.0425916600387234,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0390744040629657,0,0,0,0,0.401804113981,0.341785783760639,0.645214222244324,0.426124360120328,0.422499408609911,0.361150902956099,0.499704364577129,0.816365684940928,0,0,0,0.300635144080473,0.0585282132292033,0.154378642241007,0.414013956032441,0.446570459051034,0.348446446856288,0.493699993282781,0.361442195577449,0.428909200321987,0.281701056973614,0.435124007535533,0,0.371868115536423,0.358830056255803,0.34454911078934,0.154072694012943,0.532058111108361,0.116355582210209,0.0876664805795525,0.125057592200758,0.498209765015121,0,0,0.371488719240667,0.300859697994908,0,0,0,0,0.263983934288801,0,0,0,0,0,0,0,0,0,0.0789089986057754,0.191050583413854,0,0,0.136484150373336,0,0,0,0.244816787281235,0,0.475793526298786,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0321956448428329,0,0,0,0,0,0,0,1.15488415944543,0.35487513487941,0.221374256808514,0,0,0.0644802819135284,0,0.169324547093176,0,0,0,0,0,0,0,0.112779598617622,0.185869835237749,0.0823702229656663,0,0,0,0.39087124941973,0,0,0,0,0,0.0516822929650548,0,0,0,0,0,0,0,0,0,0,0,0.1301578714358,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0557243212092205,0,0,0.411169039094447,0,0,0,0,0,0,0,0,0,0,0,0,0,0.230849099791231,0,0,0,0,0,0.272307630936553,0.248905129112398,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.123319086035448,0,0,0,0,0,0,0,0,0.0440642112897698,0,0.350774507210926,0.650614641686925,0.252961355161605,0.345947048864674,0,0,0,0,0,0,0,0,0,0,0.0456863240084368,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0904423417827262,0,0,0,0,0,0,0,0,0,0,0,0.0879028774822819,0.145691822538464,0.0657907963604995,0,0,0,0.447140436272986,0.242253652101142,0.376160681111738,0,0,0,0,0,0,0,0,0,0,0,0,0,0.119073348236779,0,0,0,0,0,0.064320887423737,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.123048870237934,0.051298371688257,0,0,0,0,0,0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|full_id=C746_Neutrophils_chronic_Monocytederived_CD4_Whole_Hodgkin_lymph
|full_id=C746_Neutrophils_chronic_Monocytederived_CD4_Whole_Hodgkin_lymph
|gostat_on_coexpression_clusters=GO:0019982!interleukin-7 binding!0.0047242008376489!3561$GO:0004917!interleukin-7 receptor activity!0.0047242008376489!3561$GO:0004913!interleukin-4 receptor activity!0.0047242008376489!3561$GO:0019979!interleukin-4 binding!0.0047242008376489!3561$GO:0019976!interleukin-2 binding!0.0047242008376489!3561$GO:0004911!interleukin-2 receptor activity!0.0047242008376489!3561$GO:0046030!inositol trisphosphate phosphatase activity!0.00944701104561127!3635$GO:0004445!inositol-polyphosphate 5-phosphatase activity!0.00944701104561127!3635$GO:0004907!interleukin receptor activity!0.0314511171465861!3561$GO:0007165!signal transduction!0.0314511171465861!5880;3561;3635$GO:0019965!interleukin binding!0.0314511171465861!3561$GO:0006955!immune response!0.0314511171465861!3561;3635$GO:0007154!cell communication!0.0314511171465861!5880;3561;3635$GO:0030031!cell projection biogenesis!0.0314511171465861!5880$GO:0009897!external side of plasma membrane!0.0314511171465861!3561$GO:0002376!immune system process!0.0316296020883855!3561;3635$GO:0004437!inositol or phosphatidylinositol phosphatase activity!0.0316296020883855!3635$GO:0004896!hematopoietin/interferon-class (D200-domain) cytokine receptor activity!0.0361485493485189!3561$GO:0019838!growth factor binding!0.0441463508053512!3561$GO:0019955!cytokine binding!0.0466375408730237!3561
|gostat_on_coexpression_clusters=GO:0019982!interleukin-7 binding!0.0047242008376489!3561$GO:0004917!interleukin-7 receptor activity!0.0047242008376489!3561$GO:0004913!interleukin-4 receptor activity!0.0047242008376489!3561$GO:0019979!interleukin-4 binding!0.0047242008376489!3561$GO:0019976!interleukin-2 binding!0.0047242008376489!3561$GO:0004911!interleukin-2 receptor activity!0.0047242008376489!3561$GO:0046030!inositol trisphosphate phosphatase activity!0.00944701104561127!3635$GO:0004445!inositol-polyphosphate 5-phosphatase activity!0.00944701104561127!3635$GO:0004907!interleukin receptor activity!0.0314511171465861!3561$GO:0007165!signal transduction!0.0314511171465861!5880;3561;3635$GO:0019965!interleukin binding!0.0314511171465861!3561$GO:0006955!immune response!0.0314511171465861!3561;3635$GO:0007154!cell communication!0.0314511171465861!5880;3561;3635$GO:0030031!cell projection biogenesis!0.0314511171465861!5880$GO:0009897!external side of plasma membrane!0.0314511171465861!3561$GO:0002376!immune system process!0.0316296020883855!3561;3635$GO:0004437!inositol or phosphatidylinositol phosphatase activity!0.0316296020883855!3635$GO:0004896!hematopoietin/interferon-class (D200-domain) cytokine receptor activity!0.0361485493485189!3561$GO:0019838!growth factor binding!0.0441463508053512!3561$GO:0019955!cytokine binding!0.0466375408730237!3561

Revision as of 18:27, 12 September 2012


Full id: C746_Neutrophils_chronic_Monocytederived_CD4_Whole_Hodgkin_lymph



Phase1 CAGE Peaks

Hg19::chr12:15095224..15095238,-p@chr12:15095224..15095238
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Hg19::chr12:15095377..15095412,-p@chr12:15095377..15095412
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Hg19::chr12:15095596..15095637,-p@chr12:15095596..15095637
-
Hg19::chr12:15097732..15097776,-p@chr12:15097732..15097776
-
Hg19::chr16:30198754..30198769,+p@chr16:30198754..30198769
+
Hg19::chr22:37621663..37621687,-p4@RAC2
Hg19::chr2:234104079..234104082,+p4@INPP5D
Hg19::chrX:70327539..70327558,-p@chrX:70327539..70327558
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Hg19::chrX:70327608..70327641,-p@chrX:70327608..70327641
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Hg19::chrX:70327646..70327667,-p@chrX:70327646..70327667
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Hg19::chrX:70329181..70329194,-p2@IL2RG


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
2.03984814542931e-050.0047782444038979275B cell receptor signaling pathway (KEGG):04662
2.26457080753455e-050.0047782444038979279Fc epsilon RI signaling pathway (KEGG):04664
3.28059829023111e-050.00479055337409632295Fc gamma R-mediated phagocytosis (KEGG):04666
3.78400740449947e-050.004790553374096322102IL-3 Signaling Pathway (Wikipathways):WP286
1.48230348787841e-050.0047782444038979264IL-4 signaling Pathway (Wikipathways):WP395



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:0019982interleukin-7 binding0.0047242008376489
GO:0004917interleukin-7 receptor activity0.0047242008376489
GO:0004913interleukin-4 receptor activity0.0047242008376489
GO:0019979interleukin-4 binding0.0047242008376489
GO:0019976interleukin-2 binding0.0047242008376489
GO:0004911interleukin-2 receptor activity0.0047242008376489
GO:0046030inositol trisphosphate phosphatase activity0.00944701104561127
GO:0004445inositol-polyphosphate 5-phosphatase activity0.00944701104561127
GO:0004907interleukin receptor activity0.0314511171465861
GO:0007165signal transduction0.0314511171465861
GO:0019965interleukin binding0.0314511171465861
GO:0006955immune response0.0314511171465861
GO:0007154cell communication0.0314511171465861
GO:0030031cell projection biogenesis0.0314511171465861
GO:0009897external side of plasma membrane0.0314511171465861
GO:0002376immune system process0.0316296020883855
GO:0004437inositol or phosphatidylinositol phosphatase activity0.0316296020883855
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0361485493485189
GO:0019838growth factor binding0.0441463508053512
GO:0019955cytokine binding0.0466375408730237



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
hematopoietic stem cell2.03e-66172
angioblastic mesenchymal cell2.03e-66172
hematopoietic cell3.24e-64182
hematopoietic oligopotent progenitor cell6.32e-63165
hematopoietic multipotent progenitor cell6.32e-63165
leukocyte3.07e-57140
hematopoietic lineage restricted progenitor cell3.11e-48124
nongranular leukocyte8.57e-48119
myeloid cell2.50e-35112
common myeloid progenitor2.50e-35112
myeloid leukocyte2.95e-2676
lymphocyte2.31e-2453
common lymphoid progenitor2.31e-2453
lymphoid lineage restricted progenitor cell5.56e-2452
myeloid lineage restricted progenitor cell1.99e-2270
granulocyte monocyte progenitor cell2.26e-2271
macrophage dendritic cell progenitor1.17e-2165
monopoietic cell6.19e-2163
monocyte6.19e-2163
monoblast6.19e-2163
promonocyte6.19e-2163
CD14-positive, CD16-negative classical monocyte2.86e-2042
classical monocyte1.10e-1645
T cell8.94e-1325
pro-T cell8.94e-1325
mesenchymal cell4.98e-12358
connective tissue cell2.82e-11365
lymphocyte of B lineage6.34e-1124
pro-B cell6.34e-1124
mature alpha-beta T cell2.71e-1018
alpha-beta T cell2.71e-1018
immature T cell2.71e-1018
mature T cell2.71e-1018
immature alpha-beta T cell2.71e-1018
multi fate stem cell6.50e-08430
somatic stem cell1.38e-07436
stem cell2.13e-07444
B cell3.26e-0714
CD8-positive, alpha-beta T cell9.06e-0711
Uber Anatomy
Ontology termp-valuen
hemolymphoid system5.16e-29112
hematopoietic system8.52e-29102
blood island8.52e-29102
lateral plate mesoderm4.42e-21216
bone marrow2.32e-1980
immune system6.80e-17115
bone element1.28e-1586
skeletal element2.03e-10101
skeletal system2.03e-10101
connective tissue7.89e-10375
blood6.09e-0815
haemolymphatic fluid6.09e-0815
organism substance6.09e-0815
Disease
Ontology termp-valuen
hematologic cancer2.54e-1551
immune system cancer2.54e-1551
leukemia2.86e-1239
myeloid leukemia2.40e-0931


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)

{{{tfbs_overrepresentation_jaspar}}}



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.