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Coexpression cluster:C2578: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2578_Eosinophils_CD14_CD19_Neutrophils_CD4_Whole_CD14CD16
|id=C2578
}}

Latest revision as of 12:08, 17 September 2013


Full id: C2578_Eosinophils_CD14_CD19_Neutrophils_CD4_Whole_CD14CD16



Phase1 CAGE Peaks

Hg19::chr1:2487990..2488033,+p1@TNFRSF14
Hg19::chr2:231191875..231191918,+p1@SP140L
Hg19::chr2:231280908..231280945,+p1@SP100
Hg19::chr7:144533074..144533153,-p1@TPK1


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:0009229thiamin diphosphate biosynthetic process0.0052451874720812
GO:0006772thiamin metabolic process0.0052451874720812
GO:0042724thiamin and derivative biosynthetic process0.0052451874720812
GO:0042357thiamin diphosphate metabolic process0.0052451874720812
GO:0004788thiamin diphosphokinase activity0.0052451874720812
GO:0042723thiamin and derivative metabolic process0.00728455370169519
GO:0005031tumor necrosis factor receptor activity0.00971130870574048
GO:0043120tumor necrosis factor binding0.00971130870574048
GO:0005035death receptor activity0.00971130870574048
GO:0016778diphosphotransferase activity0.0122348080968153
GO:0016605PML body0.0127107404706818
GO:0006767water-soluble vitamin metabolic process0.0465402161415903



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
leukocyte4.21e-55136
hematopoietic lineage restricted progenitor cell1.69e-46120
nongranular leukocyte3.42e-46115
hematopoietic stem cell1.61e-45168
angioblastic mesenchymal cell1.61e-45168
hematopoietic cell1.76e-43177
hematopoietic oligopotent progenitor cell1.15e-42161
hematopoietic multipotent progenitor cell1.15e-42161
myeloid leukocyte1.13e-3172
granulocyte monocyte progenitor cell1.31e-2767
myeloid lineage restricted progenitor cell4.76e-2766
macrophage dendritic cell progenitor1.10e-2561
defensive cell1.78e-2548
phagocyte1.78e-2548
monopoietic cell1.94e-2559
monocyte1.94e-2559
monoblast1.94e-2559
promonocyte1.94e-2559
classical monocyte2.15e-2342
CD14-positive, CD16-negative classical monocyte2.15e-2342
myeloid cell4.79e-23108
common myeloid progenitor4.79e-23108
mesenchymal cell3.61e-21354
connective tissue cell2.89e-20361
nucleate cell2.40e-1855
lymphocyte2.78e-1853
common lymphoid progenitor2.78e-1853
lymphoid lineage restricted progenitor cell4.78e-1852
multi fate stem cell8.09e-16427
somatic stem cell4.70e-14433
motile cell3.94e-13386
stem cell4.72e-13441
mature alpha-beta T cell4.73e-1018
alpha-beta T cell4.73e-1018
immature T cell4.73e-1018
mature T cell4.73e-1018
immature alpha-beta T cell4.73e-1018
T cell1.66e-0925
pro-T cell1.66e-0925
lymphocyte of B lineage1.27e-0824
pro-B cell1.27e-0824
B cell4.45e-0814
stuff accumulating cell5.04e-0887
CD8-positive, alpha-beta T cell7.30e-0711
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.30e-35108
hematopoietic system1.40e-3498
blood island1.40e-3498
immune system6.22e-2993
bone marrow1.31e-2576
bone element8.91e-2282
skeletal element3.39e-2090
connective tissue1.49e-19371
lateral plate mesoderm1.42e-18203
skeletal system1.85e-18100
musculoskeletal system3.05e-10167
mesoderm1.41e-09315
mesoderm-derived structure1.41e-09315
presumptive mesoderm1.41e-09315
blood1.93e-0715
haemolymphatic fluid1.93e-0715
organism substance1.93e-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)
MA0003.10.233555
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
MA0028.11.35734
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
MA0055.10.791759
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
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
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.11.90157
MA0106.10.869173
MA0107.10.453492
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
MA0146.11.75643
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.12.36058
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.11.37853
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.20.0270533
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
BATF#10538212.17890089615180.009566758805047810.0360207196928541
FOS#235336.74846648167080.005032452776317940.0234698729796315
GABPB1#255335.300762877136630.01012678824234270.0378631596048413
IRF1#365947.63716375356390.0002938853996185490.00307731073298192
IRF4#3662210.95725634337210.01174530180688030.0428470283771272
NR2C2#7182216.30730545262040.005411825344648220.0245581415237765
PAX5#507935.002174148383370.01196533174786410.0435007930662852
POLR3A#11128184.78302752293580.01174284177711620.0428635066531607
PRDM1#639265.91547788873040.0003415175120768950.00346760134588751
REST#597837.237521537096020.004104697304192610.0195829556325692
SPI1#668836.153242631392040.006580387113059030.0281014495297993
SRF#6722310.34788369662590.001439893778401260.00923943636780839
STAT1#6772210.35329374859960.01310777476171260.0464937810195117
STAT2#6773232.63188559322030.001379588775125520.00898384287849694
TAF1#687243.343046285745290.008005664898701650.0322483756838625
ZBTB7A#5134135.513931980906920.009038352821081090.034247234708881



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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