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Coexpression cluster:C2306: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2306_CD4_CD8_cerebellum_Mast_Neural_thymus_Natural
|id=C2306
}}

Latest revision as of 12:03, 17 September 2013


Full id: C2306_CD4_CD8_cerebellum_Mast_Neural_thymus_Natural



Phase1 CAGE Peaks

Hg19::chr14:64108537..64108597,-p1@WDR89
Hg19::chr2:120517452..120517509,+p1@PTPN4
Hg19::chr2:120517517..120517541,+p2@PTPN4
Hg19::chr2:242041691..242041740,-p1@MTERFD2


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:0004726non-membrane spanning protein tyrosine phosphatase activity0.00927234192864712



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
nucleate cell1.15e-2155
lymphocyte5.63e-2153
common lymphoid progenitor5.63e-2153
lymphoid lineage restricted progenitor cell1.62e-2052
mature alpha-beta T cell1.89e-1218
alpha-beta T cell1.89e-1218
immature T cell1.89e-1218
mature T cell1.89e-1218
immature alpha-beta T cell1.89e-1218
T cell6.77e-1225
pro-T cell6.77e-1225
CD8-positive, alpha-beta T cell1.68e-0811
lymphocyte of B lineage2.57e-0824
pro-B cell2.57e-0824
B cell1.58e-0714
Uber Anatomy
Ontology termp-valuen
adult organism4.46e-22114
central nervous system1.48e-1381
nervous system1.72e-1289
neural tube1.55e-1156
neural rod1.55e-1156
future spinal cord1.55e-1156
neural keel1.55e-1156
regional part of nervous system2.47e-1153
regional part of brain2.47e-1153
regional part of forebrain3.12e-1141
forebrain3.12e-1141
anterior neural tube3.12e-1141
future forebrain3.12e-1141
brain3.47e-1068
future brain3.47e-1068
telencephalon5.90e-0934
organ system subdivision1.37e-08223
brain grey matter1.39e-0834
gray matter1.39e-0834
regional part of telencephalon2.35e-0832
cerebral hemisphere2.44e-0832
blood3.44e-0715
haemolymphatic fluid3.44e-0715
organism substance3.44e-0715
cerebral cortex7.95e-0725
pallium7.95e-0725


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
MA0014.10.244769
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
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.11.80156
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
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
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
MA0105.10.656404
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
MA0145.11.08195
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.20.0247757
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
MA0154.10.649108
MA0155.10.180766
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
MA0079.21.11128
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
BCLAF1#9774210.82632380506090.01202203816432580.0436507316035329
BRCA1#672315.13817298241780.0004682184421431190.00430043671435979
CHD2#1106410.34402283411698.73193255208051e-050.00128971051309113
E2F6#187645.017155731697390.00157802193473060.00995873060857629
ELF1#199744.258097958807540.003041525565781240.0160699088665264
EP300#203335.08045629466740.01144298405398240.0418802148729277
ETS1#211337.296570691651750.00400857377511390.0192015519194203
GATA1#2623310.17023110785030.001515158168498270.00966124940227066
GTF2B#2959215.97191496716210.005636585723537220.0254696221338858
GTF2F1#296239.554745657568240.001820362319304780.0108974447017008
HDAC2#3066310.06171517746970.00156372754474740.00992308549312636
HEY1#2346244.040111043105710.00375304636917980.0185738714756561
HMGN3#932448.178547723350590.0002234570284440470.00247824451456598
IRF1#365935.727872815172930.008097114790333330.0319984324045566
IRF4#3662210.95725634337210.01174530180688030.0428275810142021
JUND#372735.245997956403270.01043432751748420.0386751865563592
MAFF#23764228.15767824497260.001846876180367150.0109240471994883
MAX#414934.839416631755340.01315737137836840.0466063868330421
MEF2A#4205314.0574231822330.0005830038854186610.00488670487875116
MYC#460945.22228187160940.001344309395272740.00886520988399882
NFKB1#479045.488063424193840.001102199566301980.0076726401722997
NFYA#4800313.81918552487290.0006132411806734510.00508586481921342
NR3C1#2908311.22976749837980.001131672068063850.00775376888516177
PAX5#507946.669565531177830.0005052774169483260.00443413731187851
RFX5#5993412.04791082719514.74457429336527e-050.000825864324374626
RXRA#6256315.055962854350.0004758307997303580.00433754847630609
SETDB1#9869330.24001963350795.98509618524166e-050.000984528997464882
SMARCB1#6598313.68953683586810.0006305783409379340.0051806931520781
SP1#666745.69838137814090.0009482606065333980.00683379723197223
SPI1#668836.153242631392040.006580387113059030.0280957053963768
SREBF2#67211109.2358156028370.009123201484126820.034516139822522
SRF#6722413.79717826216782.75840773062708e-050.000583641298579743
TAF1#687243.343046285745290.008005664898701650.0321652549186544
TAF7#687938.574802053692940.00250055433515240.0140285450262667
TAL1#6886214.93430833872010.006428077577888070.0279434753031031
TBP#690843.706770687096390.005296377814784350.0243774361023429
TCF7L2#6934410.77017656313737.42969445082454e-050.00115228669252994
USF1#739146.361499277207960.0006105011399140830.00507321201078031
YY1#752844.911170749853860.00171871838055440.0106687208883638
ZBTB33#10009323.74854377248590.0001229451908818380.00165488758738346
ZEB1#6935416.88843201754391.22862303393937e-050.000303778790344683
ZNF263#1012748.221841637010680.0002187871180958320.00248260623933188



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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