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Coexpression cluster:C2869: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2869_optic_pineal_colon_breast_seminal_globus_kidney
|id=C2869
}}

Latest revision as of 12:14, 17 September 2013


Full id: C2869_optic_pineal_colon_breast_seminal_globus_kidney



Phase1 CAGE Peaks

Hg19::chr6:76458921..76458934,+p3@MYO6
Hg19::chr6:76458948..76458964,+p1@MYO6
Hg19::chr6:76458969..76458980,+p4@MYO6
Hg19::chr6:76458990..76459011,+p2@MYO6


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><br>

Cell Type
Ontology termp-valuen
epithelial cell1.98e-08253
Uber Anatomy
Ontology termp-valuen
anatomical cluster2.19e-31373
organ system subdivision1.46e-24223
anatomical conduit4.48e-24240
central nervous system4.06e-2381
neural tube5.30e-2356
neural rod5.30e-2356
future spinal cord5.30e-2356
neural keel5.30e-2356
adult organism4.93e-22114
nervous system1.78e-2189
regional part of nervous system2.04e-2153
regional part of brain2.04e-2153
brain3.92e-2168
future brain3.92e-2168
ectoderm-derived structure1.58e-20171
ectoderm1.58e-20171
presumptive ectoderm1.58e-20171
multi-cellular organism7.72e-20656
ecto-epithelium5.70e-19104
tube6.15e-19192
regional part of forebrain1.19e-1841
forebrain1.19e-1841
anterior neural tube1.19e-1841
future forebrain1.19e-1841
neural plate5.08e-1882
presumptive neural plate5.08e-1882
cell layer1.83e-17309
multi-tissue structure2.19e-17342
anatomical group2.96e-17625
anatomical system2.98e-17624
epithelium3.52e-17306
organ1.71e-15503
neurectoderm2.04e-1586
brain grey matter1.26e-1434
gray matter1.26e-1434
telencephalon1.31e-1434
pre-chordal neural plate2.86e-1461
regional part of telencephalon1.28e-1332
cerebral hemisphere1.49e-1332
structure with developmental contribution from neural crest3.32e-13132
organ part4.18e-12218
embryo2.31e-11592
regional part of cerebral cortex4.06e-1022
cerebral cortex4.08e-1025
pallium4.08e-1025
developing anatomical structure7.74e-10581
neocortex3.11e-0920
embryonic structure4.82e-08564
germ layer2.37e-07560
germ layer / neural crest2.37e-07560
embryonic tissue2.37e-07560
presumptive structure2.37e-07560
germ layer / neural crest derived structure2.37e-07560
epiblast (generic)2.37e-07560
organism subdivision2.60e-07264
immaterial anatomical entity3.86e-07117
digestive system6.64e-07145
digestive tract6.64e-07145
primitive gut6.64e-07145


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)
MA0003.16.11661
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
MA0017.10.577281
MA0019.10.873355
MA0024.12.48281
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
MA0043.12.70453
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.13.49299
MA0063.10
MA0066.10.825101
MA0067.13.36035
MA0068.10.313194
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
MA0105.13.51257
MA0106.12.01886
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
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
MA0145.11.70272
MA0146.10.481
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.65877
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.12.64806
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.00408
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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#90546.336201576962630.0006203100587215640.00513592533873644
E2F1#186944.907389214879320.001724022357361790.0106794288837786
EGR1#195844.988179094810140.001615011500076050.0101645285076801
ELF1#199744.258097958807540.003041525565781240.016125381418581
ETS1#211349.728760922202340.0001115955317418140.00154800448128347
HEY1#2346244.040111043105710.00375304636917980.0186587523087909
MYC#460945.22228187160940.001344309395272740.00889779637067554
SMARCB1#6598313.68953683586810.0006305783409379340.005182731671458
TAF1#687243.343046285745290.008005664898701650.0323281767913816
TBP#690843.706770687096390.005296377814784350.024499442049706
THAP1#55145431.36914460285131.03171810326891e-064.3256365711482e-05
ZBTB7A#5134147.35190930787590.000342223540015990.00347240690719226
ZEB1#6935416.88843201754391.22862303393937e-050.000305223979642231
ZNF263#1012748.221841637010680.0002187871180958320.00249889630651909



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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