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{{Coexpression_clusters
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|full_id=C2651_granulocyte_CD4_CD8_Small_CD19_CD34_Natural
|gostat_on_coexpression_clusters=GO:0008274!gamma-tubulin ring complex!0.0193637610957729!85378$GO:0000931!gamma-tubulin large complex!0.0193637610957729!85378$GO:0016018!cyclosporin A binding!0.0193637610957729!4820$GO:0007020!microtubule nucleation!0.0193637610957729!85378$GO:0000930!gamma-tubulin complex!0.0221270812370609!85378$GO:0008144!drug binding!0.0363307709258282!4820$GO:0044450!microtubule organizing center part!0.0363307709258282!85378$GO:0000922!spindle pole!0.0428314809153511!85378
|id=C2651
}}

Latest revision as of 12:10, 17 September 2013


Full id: C2651_granulocyte_CD4_CD8_Small_CD19_CD34_Natural



Phase1 CAGE Peaks

Hg19::chr22:50683388..50683444,-p1@TUBGCP6
Hg19::chr3:42642138..42642200,+p1@NKTR
Hg19::chr6:131949305..131949389,-p1@MED23
Hg19::chr8:100025476..100025548,+p1@VPS13B


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:0008274gamma-tubulin ring complex0.0193637610957729
GO:0000931gamma-tubulin large complex0.0193637610957729
GO:0016018cyclosporin A binding0.0193637610957729
GO:0007020microtubule nucleation0.0193637610957729
GO:0000930gamma-tubulin complex0.0221270812370609
GO:0008144drug binding0.0363307709258282
GO:0044450microtubule organizing center part0.0363307709258282
GO:0000922spindle pole0.0428314809153511



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>

Uber Anatomy
Ontology termp-valuen
adult organism6.24e-27114
neural tube1.12e-1556
neural rod1.12e-1556
future spinal cord1.12e-1556
neural keel1.12e-1556
regional part of nervous system1.18e-1453
regional part of brain1.18e-1453
regional part of forebrain2.26e-1341
forebrain2.26e-1341
anterior neural tube2.26e-1341
future forebrain2.26e-1341
brain2.59e-1368
future brain2.59e-1368
central nervous system3.37e-1281
nervous system4.34e-1289
telencephalon1.40e-1034
brain grey matter1.58e-1034
gray matter1.58e-1034
regional part of telencephalon4.65e-1032
cerebral hemisphere6.89e-1032
neurectoderm1.46e-0886
hematopoietic system2.50e-0898
blood island2.50e-0898
regional part of cerebral cortex6.34e-0822
neural plate8.48e-0882
presumptive neural plate8.48e-0882
cerebral cortex1.02e-0725
pallium1.02e-0725
neocortex2.43e-0720
hemolymphoid system3.90e-07108


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
MA0007.11.65296
MA0009.11.20602
MA0014.10.896009
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.12.32784
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
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
MA0073.10.00636811
MA0074.10.819248
MA0076.12.5647
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
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
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
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.11.75643
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.22.51225
MA0035.20.778873
MA0039.20.257871
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
MA0155.11.02191
MA0156.12.36058
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.122011
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
ATF3#467211.23158726300440.01119559039922220.0411318910087018
BCLAF1#9774210.82632380506090.01202203816432580.0436613570206913
BRCA1#672210.09211532161190.0137713969900260.0484755958962361
CCNT2#90534.752151182721970.01386206996689490.0487307120829558
CHD2#110637.758017125587640.003351522464536340.017302503938394
ELF1#199744.258097958807540.003041525565781240.0161065758323003
ELK4#2005312.1767612438510.0008912632577620610.00663832858204335
GABPB1#255335.300762877136630.01012678824234270.0378712943474785
HEY1#2346244.040111043105710.00375304636917980.0186312581876019
HMGN3#932436.133910792512940.006640696683324720.0283034492699049
IRF4#3662210.95725634337210.01174530180688030.0428575073512953
JUND#372735.245997956403270.01043432751748420.0387026576552379
MEF2A#4205314.0574231822330.0005830038854186610.00488866662298189
MXI1#460137.471178721569470.003741314738550960.0186376899584795
PAX5#507935.002174148383370.01196533174786410.0435083657967821
POU2F2#545236.829593043306890.004860473775203740.0227664269008612
REST#597837.237521537096020.004104697304192610.019585639699953
SIN3A#2594245.408884726815140.001168172384885160.00797143127768839
SIX5#147912312.81503651659420.0007664471136930380.00601721191513096
STAT2#6773232.63188559322030.001379588775125520.00898496333782327
TAF1#687243.343046285745290.008005664898701650.0322670437000425
TBP#690843.706770687096390.005296377814784350.0244571960294585
TCF7L2#6934410.77017656313737.42969445082454e-050.00115554707185356
THAP1#55145215.68457230142570.005840469678357920.026250067252142
USF1#739134.771124457905970.01370465887188020.0483139533475204
YY1#752844.911170749853860.00171871838055440.010694782468227
ZBTB33#10009215.83236251499060.005734248930324640.0258416062150669
ZEB1#6935312.66632401315790.000793336075912850.00613288130512674



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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