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Coexpression cluster:C2859: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.226854972210666,0.297434101672374,0.242369780872192,0.0720323359375575,0.194240495619742,0.0625128387853364,0,0,0,0,0,0,0,0.247539261412231,0.0426472287497177,0,0,0,0.029478255492678,0.0696050589321335,0.0471628892761728,0,0,0.0585869700440155,0,0,0.0460939396382715,0.113877987764218,0,0,0,0,0,0.057985536717467,0.0604397418968705,0,0,0.0394935469382982,0.077093984435699,0.055330073681763,0,0,0.0486718136065485,0,0,0,0,0,0.0832356854652995,0,0,0,0,0.0647295580076124,0,0,0,0,0.094624212904935,0,0,0,0,0,0,0.195681888795628,0.729018013591892,0.553868652925089,0,0.214190980924287,0,0,0.071977235952296,0,0.033570127014991,0,0,0,0.0458744785985099,0,0,0.0520392632952425,0,0.0502057274031015,0.0330581670420442,0,0.055261705806051,0.0300251414480776,0,0,0,0.0704457073800035,0,0,0,0,0,0.0304574891363872,0,0,0,0,0.0398811784290288,0.312104029121882,0.08460516978145,0,0,0,0,0,0,0,0,0,0,0,0.0137745948241495,0,0,0.12206750241012,0.0997447842452864,0.16549482722259,0.869988860798555,0.840700634307317,0.558800780780323,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.096656598571488,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0214178589168123,0,0.13512544777972,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0343837153039546,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.040912657171121,0.0292357798753831,0,0.0512318647957875,0,0.336894705459779,0.322782306059375,0.058383955688522,0,0.189053165702156,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0439209172336585,0.208498394750677,0.459354363064166,0.268618726544372,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0848314897427103,0.0440407241264263,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0200381238622658,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.089121113667536,0,0,0.13101233739175,0.07481925209622,0,0,0,0,0,0,0.360424323905713,0.0843127937780741,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0296885786825552,0,0.513397064014485,0,0,0,0,0,0,0,0.331895180683571,0,0,0.095525291706927,0,0,0.310755990297353,0,0,0,0.089714472461443,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0223967159144265,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0184057509736802,0,0.67344564383158,0.580515494464835,0.550826009541936,0,0,0,0.162348236648676,0,0,0,0,0,0.0133047429825382,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.387807179894788,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0679432810511184,0,0,0,0,0,0.267626233082973,0,0,0,0,0.0111016828724432,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0264013868126934,0,0,0,0,0,0,0,0.560424726561789,0.240599942298114,0,0,0,0,0,0,0,0,0,0,0,0.0130819689967123,0,0,0,0,0,0,0,0,0,0.095838084610127,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.844715967049689,0.619133007961953,0.81496985303158,0,0,0,0.200690278211263,0,0.800550352632849,0,0,0,0,0,0,0,0,0,0,0,0,0,0.144358945011604,0,0,0,0.0135175905173599,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.018454584201652,0.294890985784283,0,0,0,0,0,0,0,0,0,0,0,0.0299826682885844,0,0,0.034807832411276,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.108403331880639,0,0,0,0,0,0,0,0,0,0.0161429629723438,0,0,0,0,0,0,0,0,0,0.0135642422894877,0.393230786176804,0,0,0,0,0.141362994159115,0,0,0,0,0,0,0,0,0,0.0225177670469836,0,0,0,0,0,0,0,0,0,0,0,0,0.068747994548089,0,0,0,0,0,0.0518006517629135,0.0150411145536097,0,0,0,0,0,0,0,0,0,0.0796420028184954,0.535593374258625|full_id=C2859_Dendritic_migratory_myeloma_adult_lymphangiectasia_xeroderma_cord|gostat_on_coexpression_clusters=GO:0045368!positive regulation of interleukin-13 biosynthetic process!0.00213699113631954!3662$GO:0045366!regulation of interleukin-13 biosynthetic process!0.00213699113631954!3662$GO:0045082!positive regulation of interleukin-10 biosynthetic process!0.00213699113631954!3662$GO:0042231!interleukin-13 biosynthetic process!0.00213699113631954!3662$GO:0045074!regulation of interleukin-10 biosynthetic process!0.00213699113631954!3662$GO:0032616!interleukin-13 production!0.00213699113631954!3662$GO:0045404!positive regulation of interleukin-4 biosynthetic process!0.00213699113631954!3662$GO:0042091!interleukin-10 biosynthetic process!0.00213699113631954!3662$GO:0042097!interleukin-4 biosynthetic process!0.00213699113631954!3662$GO:0045402!regulation of interleukin-4 biosynthetic process!0.00213699113631954!3662$GO:0032633!interleukin-4 production!0.00259025416027356!3662$GO:0032613!interleukin-10 production!0.00296795587240533!3662$GO:0045622!regulation of T-helper cell differentiation!0.00339169993279774!3662$GO:0002285!lymphocyte activation during immune response!0.00339169993279774!3662$GO:0002293!alpha-beta T cell differentiation during immune response!0.00339169993279774!3662$GO:0002294!CD4-positive, alpha-beta T cell differentiation during immune response!0.00339169993279774!3662$GO:0002292!T cell differentiation during immune response!0.00339169993279774!3662$GO:0042093!T-helper cell differentiation!0.00339169993279774!3662$GO:0002366!leukocyte activation during immune response!0.00339169993279774!3662$GO:0002286!T cell activation during immune response!0.00339169993279774!3662$GO:0002263!cell activation during immune response!0.00339169993279774!3662$GO:0043367!CD4-positive, alpha beta T cell differentiation!0.0034063963100371!3662$GO:0045086!positive regulation of interleukin-2 biosynthetic process!0.0034063963100371!3662$GO:0045076!regulation of interleukin-2 biosynthetic process!0.00438273278584504!3662$GO:0046632!alpha-beta T cell differentiation!0.00438273278584504!3662$GO:0042094!interleukin-2 biosynthetic process!0.00438273278584504!3662$GO:0046631!alpha-beta T cell activation!0.00501151475870867!3662$GO:0032623!interleukin-2 production!0.00534106240657551!3662$GO:0042108!positive regulation of cytokine biosynthetic process!0.00972973679009771!3662$GO:0030217!T cell differentiation!0.00972973679009771!3662$GO:0045727!positive regulation of translation!0.0121695889114223!3662$GO:0042035!regulation of cytokine biosynthetic process!0.0129405954725452!3662$GO:0031328!positive regulation of cellular biosynthetic process!0.0129405954725452!3662$GO:0030098!lymphocyte differentiation!0.0133965329354952!3662$GO:0042089!cytokine biosynthetic process!0.0134422564976761!3662$GO:0042107!cytokine metabolic process!0.0134422564976761!3662$GO:0009891!positive regulation of biosynthetic process!0.0134632306164145!3662$GO:0051247!positive regulation of protein metabolic process!0.0159144746976325!3662$GO:0002521!leukocyte differentiation!0.01641734330888!3662$GO:0042110!T cell activation!0.0174276911454626!3662$GO:0001816!cytokine production!0.0196007336599614!3662$GO:0045595!regulation of cell differentiation!0.0243720698181301!3662$GO:0046649!lymphocyte activation!0.0256195788897962!3662$GO:0030097!hemopoiesis!0.0260042002809116!3662$GO:0048534!hemopoietic or lymphoid organ development!0.0272332515236904!3662$GO:0045321!leukocyte activation!0.0272332515236904!3662$GO:0002520!immune system development!0.0272332515236904!3662$GO:0006417!regulation of translation!0.0272332515236904!3662$GO:0031326!regulation of cellular biosynthetic process!0.0288458775953045!3662$GO:0001775!cell activation!0.0292418842593038!3662$GO:0007169!transmembrane receptor protein tyrosine kinase signaling pathway!0.0292418842593038!2889$GO:0009889!regulation of biosynthetic process!0.0296324622673738!3662$GO:0050793!regulation of developmental process!0.0316100824187841!3662$GO:0003702!RNA polymerase II transcription factor activity!0.0359877839994034!3662$GO:0045941!positive regulation of transcription!0.0359877839994034!3662$GO:0045935!positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0366065852216123!3662$GO:0007167!enzyme linked receptor protein signaling pathway!0.037138765578115!2889$GO:0016563!transcription activator activity!0.037138765578115!3662$GO:0005085!guanyl-nucleotide exchange factor activity!0.037138765578115!2889$GO:0031325!positive regulation of cellular metabolic process!0.0431025408519966!3662$GO:0009893!positive regulation of metabolic process!0.0453984533678038!3662$GO:0051246!regulation of protein metabolic process!0.0481854091161337!3662$GO:0008134!transcription factor 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|full_id=C2859_Dendritic_migratory_myeloma_adult_lymphangiectasia_xeroderma_cord
|id=C2859
}}

Latest revision as of 12:14, 17 September 2013


Full id: C2859_Dendritic_migratory_myeloma_adult_lymphangiectasia_xeroderma_cord



Phase1 CAGE Peaks

Hg19::chr6:391743..391759,+p1@IRF4
Hg19::chr6:405020..405033,+p@chr6:405020..405033
+
Hg19::chr6:407517..407528,+p@chr6:407517..407528
+
Hg19::chr9:134497381..134497402,-p6@RAPGEF1


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:0045368positive regulation of interleukin-13 biosynthetic process0.00213699113631954
GO:0045366regulation of interleukin-13 biosynthetic process0.00213699113631954
GO:0045082positive regulation of interleukin-10 biosynthetic process0.00213699113631954
GO:0042231interleukin-13 biosynthetic process0.00213699113631954
GO:0045074regulation of interleukin-10 biosynthetic process0.00213699113631954
GO:0032616interleukin-13 production0.00213699113631954
GO:0045404positive regulation of interleukin-4 biosynthetic process0.00213699113631954
GO:0042091interleukin-10 biosynthetic process0.00213699113631954
GO:0042097interleukin-4 biosynthetic process0.00213699113631954
GO:0045402regulation of interleukin-4 biosynthetic process0.00213699113631954
GO:0032633interleukin-4 production0.00259025416027356
GO:0032613interleukin-10 production0.00296795587240533
GO:0045622regulation of T-helper cell differentiation0.00339169993279774
GO:0002285lymphocyte activation during immune response0.00339169993279774
GO:0002293alpha-beta T cell differentiation during immune response0.00339169993279774
GO:0002294CD4-positive, alpha-beta T cell differentiation during immune response0.00339169993279774
GO:0002292T cell differentiation during immune response0.00339169993279774
GO:0042093T-helper cell differentiation0.00339169993279774
GO:0002366leukocyte activation during immune response0.00339169993279774
GO:0002286T cell activation during immune response0.00339169993279774
GO:0002263cell activation during immune response0.00339169993279774
GO:0043367CD4-positive, alpha beta T cell differentiation0.0034063963100371
GO:0045086positive regulation of interleukin-2 biosynthetic process0.0034063963100371
GO:0045076regulation of interleukin-2 biosynthetic process0.00438273278584504
GO:0046632alpha-beta T cell differentiation0.00438273278584504
GO:0042094interleukin-2 biosynthetic process0.00438273278584504
GO:0046631alpha-beta T cell activation0.00501151475870867
GO:0032623interleukin-2 production0.00534106240657551
GO:0042108positive regulation of cytokine biosynthetic process0.00972973679009771
GO:0030217T cell differentiation0.00972973679009771
GO:0045727positive regulation of translation0.0121695889114223
GO:0042035regulation of cytokine biosynthetic process0.0129405954725452
GO:0031328positive regulation of cellular biosynthetic process0.0129405954725452
GO:0030098lymphocyte differentiation0.0133965329354952
GO:0042089cytokine biosynthetic process0.0134422564976761
GO:0042107cytokine metabolic process0.0134422564976761
GO:0009891positive regulation of biosynthetic process0.0134632306164145
GO:0051247positive regulation of protein metabolic process0.0159144746976325
GO:0002521leukocyte differentiation0.01641734330888
GO:0042110T cell activation0.0174276911454626
GO:0001816cytokine production0.0196007336599614
GO:0045595regulation of cell differentiation0.0243720698181301
GO:0046649lymphocyte activation0.0256195788897962
GO:0030097hemopoiesis0.0260042002809116
GO:0048534hemopoietic or lymphoid organ development0.0272332515236904
GO:0045321leukocyte activation0.0272332515236904
GO:0002520immune system development0.0272332515236904
GO:0006417regulation of translation0.0272332515236904
GO:0031326regulation of cellular biosynthetic process0.0288458775953045
GO:0001775cell activation0.0292418842593038
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0292418842593038
GO:0009889regulation of biosynthetic process0.0296324622673738
GO:0050793regulation of developmental process0.0316100824187841
GO:0003702RNA polymerase II transcription factor activity0.0359877839994034
GO:0045941positive regulation of transcription0.0359877839994034
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0366065852216123
GO:0007167enzyme linked receptor protein signaling pathway0.037138765578115
GO:0016563transcription activator activity0.037138765578115
GO:0005085guanyl-nucleotide exchange factor activity0.037138765578115
GO:0031325positive regulation of cellular metabolic process0.0431025408519966
GO:0009893positive regulation of metabolic process0.0453984533678038
GO:0051246regulation of protein metabolic process0.0481854091161337
GO:0008134transcription factor binding0.0485370818298729



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
leukocyte5.47e-39136
hematopoietic cell6.15e-31177
nongranular leukocyte4.63e-30115
hematopoietic stem cell2.50e-29168
angioblastic mesenchymal cell2.50e-29168
hematopoietic lineage restricted progenitor cell5.37e-28120
hematopoietic oligopotent progenitor cell3.57e-26161
hematopoietic multipotent progenitor cell3.57e-26161
lymphocyte1.65e-2553
common lymphoid progenitor1.65e-2553
nucleate cell3.12e-2455
lymphoid lineage restricted progenitor cell4.25e-2452
dendritic cell6.18e-1810
lymphocyte of B lineage1.25e-1524
pro-B cell1.25e-1524
conventional dendritic cell3.90e-148
myeloid leukocyte1.46e-0872
immature conventional dendritic cell1.79e-085
common dendritic progenitor1.79e-085
circulating cell2.00e-086
granulocyte monocyte progenitor cell8.09e-0867
plasmacytoid dendritic cell1.56e-073
Langerhans cell2.18e-075
macrophage dendritic cell progenitor2.25e-0761
myeloid lineage restricted progenitor cell4.35e-0766
myeloid cell5.02e-07108
common myeloid progenitor5.02e-07108
natural killer cell5.43e-073
pro-NK cell5.43e-073
T cell7.66e-0725
pro-T cell7.66e-0725
monopoietic cell7.91e-0759
monocyte7.91e-0759
monoblast7.91e-0759
promonocyte7.91e-0759
motile cell8.53e-07386
classical monocyte8.90e-0742
CD14-positive, CD16-negative classical monocyte8.90e-0742
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.57e-1598
blood island6.57e-1598
hemolymphoid system1.55e-13108
immune system5.87e-0993
blood3.78e-0715
haemolymphatic fluid3.78e-0715
organism substance3.78e-0715
bone marrow3.96e-0776
Disease
Ontology termp-valuen
lymphoma3.44e-0910


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)
MA0003.10.720743
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.11.6149
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.657636
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
ZNF274#107821355.4365384615380.002810497640394540.0153855521053132



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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