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Coexpression cluster:C2238: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2238_cerebellum_spinal_occipital_parietal_putamen_medial_middle
|id=C2238
}}

Latest revision as of 12:01, 17 September 2013


Full id: C2238_cerebellum_spinal_occipital_parietal_putamen_medial_middle



Phase1 CAGE Peaks

Hg19::chr12:72058060..72058101,+p5@THAP2
Hg19::chr7:64023410..64023428,-p2@ZNF680
Hg19::chr7:64023441..64023462,-p1@ZNF680
Hg19::chr7:64254793..64254813,+p1@ZNF138


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:0003677DNA binding0.0403705274123335
GO:0008270zinc ion binding0.0403705274123335
GO:0046914transition metal ion binding0.0440143862349641
GO:0005634nucleus0.0472393264798422
GO:0003676nucleic acid binding0.0472393264798422
GO:0043169cation binding0.0472393264798422
GO:0046872metal ion binding0.0472393264798422
GO:0043167ion binding0.0472393264798422



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
lymphocyte2.13e-1053
common lymphoid progenitor2.13e-1053
lymphoid lineage restricted progenitor cell5.49e-1052
nucleate cell8.96e-1055
Uber Anatomy
Ontology termp-valuen
adult organism2.56e-31114
central nervous system3.12e-3181
nervous system4.06e-3089
neural tube2.89e-2856
neural rod2.89e-2856
future spinal cord2.89e-2856
neural keel2.89e-2856
regional part of nervous system1.14e-2653
regional part of brain1.14e-2653
brain8.14e-2668
future brain8.14e-2668
regional part of forebrain3.34e-2441
forebrain3.34e-2441
anterior neural tube3.34e-2441
future forebrain3.34e-2441
brain grey matter2.99e-2034
gray matter2.99e-2034
telencephalon4.91e-2034
neurectoderm6.33e-2086
neural plate2.70e-1982
presumptive neural plate2.70e-1982
regional part of telencephalon5.34e-1932
cerebral hemisphere6.84e-1932
pre-chordal neural plate4.77e-1661
cerebral cortex1.38e-1425
pallium1.38e-1425
regional part of cerebral cortex5.33e-1422
organ system subdivision8.38e-13223
neocortex9.67e-1320
ecto-epithelium1.27e-12104
ectoderm-derived structure1.65e-12171
ectoderm1.65e-12171
presumptive ectoderm1.65e-12171
structure with developmental contribution from neural crest6.66e-10132
basal ganglion3.21e-079
nuclear complex of neuraxis3.21e-079
aggregate regional part of brain3.21e-079
collection of basal ganglia3.21e-079
cerebral subcortex3.21e-079
neural nucleus3.57e-079
nucleus of brain3.57e-079
Disease
Ontology termp-valuen
cancer2.09e-11235
disease of cellular proliferation1.12e-10239
organ system cancer5.88e-09137
hematologic cancer1.14e-0751
immune system cancer1.14e-0751
leukemia2.09e-0739


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)
MA0003.10.0214529
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
MA0048.12.02223
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.8712
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.12.70115
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.12.5647
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.70272
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.21.83323
MA0039.20.257871
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
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.20937
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#9774210.82632380506090.01202203816432580.0436476967198784
CHD2#1106410.34402283411698.73193255208051e-050.0012893458275226
E2F4#187439.501045236463330.001850751034728270.0109246926646688
ELF1#199744.258097958807540.003041525565781240.0160658450619374
FOS#235336.74846648167080.005032452776317940.0234583501676353
GABPB1#255347.067683836182170.0004006876864423170.00389894915534791
HEY1#2346244.040111043105710.00375304636917980.0185668329188939
IRF1#365947.63716375356390.0002938853996185490.00306992370981813
IRF3#3661335.23646415861723.79279212646878e-050.000719555707350178
NFYA#4800313.81918552487290.0006132411806734510.00508505721860695
NFYB#4801312.56984494015230.000811456397697350.00618506018968863
PBX3#5090316.43588451505810.0003669431395554610.00365679146488863
RFX5#5993412.04791082719514.74457429336527e-050.000825726703257416
SIN3A#2594245.408884726815140.001168172384885160.00794909797400448
SP1#666745.69838137814090.0009482606065333980.00683332570797913
SP2#6668319.61514787038350.0002171004269245340.00248506701968121
SPI1#668836.153242631392040.006580387113059030.0280945568514746
TAF1#687243.343046285745290.008005664898701650.0321491766199678
TBP#690843.706770687096390.005296377814784350.0243688445569524
TCF7L2#6934410.77017656313737.42969445082454e-050.00115194456465211
ZNF263#1012736.166381227758010.006539814347975980.0279636303250057



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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