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{{Coexpression_clusters
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|full_id=C1364_Hepatocyte_liver_occipital_cerebellum_somatostatinoma_small_pancreas
|id=C1364
}}

Latest revision as of 11:43, 17 September 2013


Full id: C1364_Hepatocyte_liver_occipital_cerebellum_somatostatinoma_small_pancreas



Phase1 CAGE Peaks

Hg19::chr12:56881874..56881907,-p4@GLS2
Hg19::chr12:56881909..56881935,-p3@GLS2
Hg19::chr12:56881937..56881963,-p2@GLS2
Hg19::chr12:56881973..56881980,-p6@GLS2
Hg19::chr12:56882118..56882125,-p9@GLS2
Hg19::chr12:56882136..56882197,-p1@GLS2


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
neural tube2.57e-3556
neural rod2.57e-3556
future spinal cord2.57e-3556
neural keel2.57e-3556
adult organism5.10e-35114
regional part of nervous system3.08e-3353
regional part of brain3.08e-3353
central nervous system4.89e-3281
organ system subdivision5.10e-32223
nervous system9.63e-3289
brain1.42e-2968
future brain1.42e-2968
regional part of forebrain1.03e-2841
forebrain1.03e-2841
anterior neural tube1.03e-2841
future forebrain1.03e-2841
brain grey matter1.38e-2334
gray matter1.38e-2334
telencephalon2.56e-2334
cerebral hemisphere1.16e-2232
regional part of telencephalon6.24e-2232
neural plate1.83e-2182
presumptive neural plate1.83e-2182
regional part of cerebral cortex1.98e-2022
neurectoderm4.10e-2086
ecto-epithelium4.54e-19104
neocortex7.19e-1920
pre-chordal neural plate2.67e-1861
ectoderm-derived structure1.18e-17171
ectoderm1.18e-17171
presumptive ectoderm1.18e-17171
cerebral cortex7.24e-1725
pallium7.24e-1725
anatomical cluster1.99e-12373
structure with developmental contribution from neural crest1.76e-09132
anatomical conduit6.18e-09240
tube1.05e-08192
multi-tissue structure1.96e-08342
neural nucleus3.20e-089
nucleus of brain3.20e-089
basal ganglion3.41e-089
nuclear complex of neuraxis3.41e-089
aggregate regional part of brain3.41e-089
collection of basal ganglia3.41e-089
cerebral subcortex3.41e-089
subdivision of digestive tract4.23e-08118
posterior neural tube6.87e-0815
chordal neural plate6.87e-0815
gyrus3.95e-076
temporal lobe5.55e-076
gland6.39e-0759
organ6.55e-07503
diencephalon7.95e-077
future diencephalon7.95e-077
digestive system9.93e-07145
digestive tract9.93e-07145
primitive gut9.93e-07145
Disease
Ontology termp-valuen
carcinoma8.78e-10106
cell type cancer3.30e-09143


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)
MA0003.10.321379
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.12.69832
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.737586
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.18.38358
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.11.80244
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.12.21033
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.14.14294
MA0106.15.46746
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.12.32339
MA0146.10.0213085
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.23.75773
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.101413
MA0065.22.35074
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.11.60937
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.13.2961
MA0160.10.600559
MA0161.10
MA0162.11.39622
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.26.53042
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
CEBPB#105167.971147625824823.89609159898068e-060.000126959098441792
E2F1#186964.907389214879327.15746523583771e-050.00112662925661742
EGR1#195864.988179094810146.48943962979974e-050.00105470056877786
ELF1#199753.548414965672950.003446837775721690.0175251589727179
FOS#235368.99795530889441.88302066097805e-066.93933644360926e-05
MAX#414955.377129590839270.000467001558889580.00429454748691281
MYC#460954.35190155967450.001297956345724110.00869681547386159
NFYA#4800618.42558069983052.55187028850458e-081.77321876953513e-06
NFYB#4801411.17319550235760.0001723343348218770.00209943142359291
PBX3#5090621.91451268674419.01304984425575e-096.89607262039726e-07
SETDB1#9869640.32002617801052.32000395126066e-102.37781052665076e-08
SP1#666765.69838137814092.91961319085282e-050.0006093554796952
SP2#6668626.15353049384463.11839597221971e-092.60545725554123e-07
SUZ12#23512433.41052060737532.29902183370319e-068.18641463655395e-05
ZNF263#1012768.221841637010683.23542093046082e-060.000108685791751817



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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