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Coexpression cluster:C2180: Difference between revisions

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{{Coexpression_clusters
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DNA binding!0.0150498688801005!26277$GO:0007004!telomere maintenance via telomerase!0.0150498688801005!26277$GO:0004004!ATP-dependent RNA helicase activity!0.0150498688801005!9785$GO:0008186!RNA-dependent ATPase activity!0.0150498688801005!9785$GO:0032200!telomere organization and biogenesis!0.0150498688801005!26277$GO:0000723!telomere maintenance!0.0150498688801005!26277$GO:0003724!RNA helicase activity!0.0150498688801005!9785$GO:0000781!chromosome, telomeric region!0.0150498688801005!26277$GO:0006278!RNA-dependent DNA replication!0.0226427060366972!26277$GO:0000375!RNA splicing, via transesterification reactions!0.0226427060366972!9785$GO:0000398!nuclear mRNA splicing, via spliceosome!0.0226427060366972!9785$GO:0000377!RNA splicing, via transesterification reactions with bulged adenosine as 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|full_id=C2180_Eosinophils_CD14_Neutrophils_CD19_Natural_Basophils_CD4
|id=C2180
}}

Latest revision as of 12:00, 17 September 2013


Full id: C2180_Eosinophils_CD14_Neutrophils_CD19_Natural_Basophils_CD4



Phase1 CAGE Peaks

Hg19::chr12:105501983..105502018,-p@chr12:105501983..105502018
-
Hg19::chr14:24711806..24711861,-p1@TINF2
Hg19::chr15:45003504..45003582,-p1@PATL2
Hg19::chr16:72127670..72127755,+p2@DHX38


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:0042162telomeric DNA binding0.0150498688801005
GO:0007004telomere maintenance via telomerase0.0150498688801005
GO:0004004ATP-dependent RNA helicase activity0.0150498688801005
GO:0008186RNA-dependent ATPase activity0.0150498688801005
GO:0032200telomere organization and biogenesis0.0150498688801005
GO:0000723telomere maintenance0.0150498688801005
GO:0003724RNA helicase activity0.0150498688801005
GO:0000781chromosome, telomeric region0.0150498688801005
GO:0006278RNA-dependent DNA replication0.0226427060366972
GO:0000375RNA splicing, via transesterification reactions0.0226427060366972
GO:0000398nuclear mRNA splicing, via spliceosome0.0226427060366972
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0226427060366972
GO:0005681spliceosome0.0414611412249278



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
leukocyte3.16e-65136
hematopoietic stem cell2.02e-57168
angioblastic mesenchymal cell2.02e-57168
hematopoietic cell7.53e-55177
hematopoietic lineage restricted progenitor cell1.81e-54120
hematopoietic oligopotent progenitor cell1.94e-53161
hematopoietic multipotent progenitor cell1.94e-53161
nongranular leukocyte2.23e-53115
myeloid leukocyte2.73e-3472
granulocyte monocyte progenitor cell2.63e-3067
myeloid lineage restricted progenitor cell4.14e-2966
myeloid cell2.98e-28108
common myeloid progenitor2.98e-28108
macrophage dendritic cell progenitor5.22e-2861
defensive cell3.12e-2748
phagocyte3.12e-2748
monopoietic cell3.57e-2759
monocyte3.57e-2759
monoblast3.57e-2759
promonocyte3.57e-2759
classical monocyte1.55e-2542
CD14-positive, CD16-negative classical monocyte1.55e-2542
nucleate cell3.51e-2355
lymphocyte4.00e-2353
common lymphoid progenitor4.00e-2353
lymphoid lineage restricted progenitor cell9.28e-2352
mesenchymal cell2.35e-18354
connective tissue cell1.78e-16361
motile cell1.32e-13386
multi fate stem cell3.41e-13427
somatic stem cell1.20e-11433
T cell2.17e-1125
pro-T cell2.17e-1125
stem cell5.71e-11441
lymphocyte of B lineage7.33e-1124
pro-B cell7.33e-1124
mature alpha-beta T cell4.18e-1018
alpha-beta T cell4.18e-1018
immature T cell4.18e-1018
mature T cell4.18e-1018
immature alpha-beta T cell4.18e-1018
B cell1.69e-0814
stuff accumulating cell1.83e-0887
Uber Anatomy
Ontology termp-valuen
hemolymphoid system8.18e-39108
hematopoietic system2.86e-3898
blood island2.86e-3898
immune system9.66e-3293
bone marrow1.24e-2876
bone element4.53e-2682
lateral plate mesoderm1.53e-22203
skeletal element1.67e-2090
skeletal system5.17e-17100
connective tissue4.95e-15371
blood1.00e-0715
haemolymphatic fluid1.00e-0715
organism substance1.00e-0715


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0050.11.66718
MA0051.11.91805
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.11.22348
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
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
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
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0021048
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
BCL3#602217.27355140186920.004834494208076070.0226721931116864
CHD2#110637.758017125587640.003351522464536340.0172905381680355
EP300#203335.08045629466740.01144298405398240.0418728780215783
FOS#235336.74846648167080.005032452776317940.0234541628589348
GTF2B#2959215.97191496716210.005636585723537220.0254685202206673
IRF1#365935.727872815172930.008097114790333330.0319935900267714
IRF3#3661223.49097610574480.002641101425375540.0145920748963019
MAX#414934.839416631755340.01315737137836840.0465953243153984
NANOG#79923214.62238924050630.006698757715363760.0284811739551732
NFYA#4800313.81918552487290.0006132411806734510.00508424987444269
NFYB#4801312.56984494015230.000811456397697350.00618415752474559
NR2C2#7182216.30730545262040.005411825344648220.0245517408961259
REST#597837.237521537096020.004104697304192610.0195713331698581
RFX5#599339.035933120396320.002144561191324070.0123818799414392
SIN3A#2594245.408884726815140.001168172384885160.00794599164419831
STAT1#6772315.52994062289940.000434088655175550.00404892248440468
STAT2#6773232.63188559322030.001379588775125520.00898216271338034
TAF1#687243.343046285745290.008005664898701650.0321355844552042
TFAP2A#7020312.38897577978370.000846941303588430.00637963958207516
USF1#739134.771124457905970.01370465887188020.0482797297416276
USF2#739239.74414803880220.001718341848410070.0107147832292137



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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