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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 12:08, 17 September 2013


Full id: C2555_Mast_brain_Hepatic_thymus_optic_cervical_corpus



Phase1 CAGE Peaks

Hg19::chr1:204463845..204463857,-p3@PIK3C2B
Hg19::chr1:204463865..204463876,-p4@PIK3C2B
Hg19::chr1:204463880..204463915,-p2@PIK3C2B
Hg19::chr1:204463918..204463963,-p1@PIK3C2B


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

No GOStat results

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
endothelial cell2.61e-0736
endothelial cell of vascular tree2.80e-0724
epithelial cell4.10e-07253
Uber Anatomy
Ontology termp-valuen
adult organism1.24e-30114
neural tube1.82e-1756
neural rod1.82e-1756
future spinal cord1.82e-1756
neural keel1.82e-1756
organ system subdivision1.28e-16223
regional part of nervous system4.74e-1653
regional part of brain4.74e-1653
regional part of forebrain4.81e-1441
forebrain4.81e-1441
anterior neural tube4.81e-1441
future forebrain4.81e-1441
central nervous system7.75e-1481
nervous system6.65e-1389
brain1.92e-1268
future brain1.92e-1268
brain grey matter2.56e-1234
gray matter2.56e-1234
telencephalon2.66e-1234
neurectoderm3.97e-1286
neural plate4.43e-1282
presumptive neural plate4.43e-1282
regional part of telencephalon2.85e-1132
cerebral hemisphere4.32e-1132
organ part7.98e-11218
anatomical cluster2.27e-10373
regional part of cerebral cortex3.39e-1022
neocortex1.43e-0920
subdivision of digestive tract3.25e-09118
pre-chordal neural plate8.70e-0961
cerebral cortex2.44e-0825
pallium2.44e-0825
anatomical conduit2.55e-08240
foregut1.55e-0787
tube2.06e-07192
Disease
Ontology termp-valuen
carcinoma8.91e-07106


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)
MA0003.11.8989
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.13.08565
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
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
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.13.24355
MA0056.10
MA0057.15.56554
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
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
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
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
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.16.90001
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.22.43626
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
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.22.02192
MA0099.20.7872
MA0079.27.57064
MA0102.21.75932
MA0258.11.88931
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
CCNT2#90546.336201576962630.0006203100587215640.00512455008881676
CTCF#1066445.360256373075030.001211145381643620.00817652311011495
CTCFL#140690419.74647435897446.5732084880439e-060.000193053802385494
E2F1#186944.907389214879320.001724022357361790.0106535217431222
E2F6#187645.017155731697390.00157802193473060.00997259063544288
EGR1#195844.988179094810140.001615011500076050.0101486273198822
ELF1#199744.258097958807540.003041525565781240.0160975973528924
GABPB1#255347.067683836182170.0004006876864423170.00390440579253117
HEY1#2346244.040111043105710.00375304636917980.0186188680292024
HMGN3#932448.178547723350590.0002234570284440470.0024819343394308
MAX#414946.452555509007120.0005767613195645490.00485659723083141
MYC#460945.22228187160940.001344309395272740.0088814732371514
NANOG#79923429.24477848101271.36586687657858e-065.33868902406402e-05
NFKB1#479045.488063424193840.001102199566301980.00768185655689104
NR3C1#2908414.9730233311731.98868032687801e-050.000443415424122144
NRF1#4899412.21027944771094.49717228915276e-050.000794317904121132
PAX5#507946.669565531177830.0005052774169483260.00444122775194969
RAD21#5885410.35503389545638.6948481184721e-050.00129466957890663
SIN3A#2594245.408884726815140.001168172384885160.00796778707582424
SMARCB1#6598418.25271578115749.00423392720929e-060.000241684190985302
SMC3#9126415.04493284493281.95092670935632e-050.000438083927324156
TAF1#687243.343046285745290.008005664898701650.0322446446724065
TBP#690843.706770687096390.005296377814784350.0244409863290148
YY1#752844.911170749853860.00171871838055440.0106909606281549
ZNF263#1012748.221841637010680.0002187871180958320.00249045316913467



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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