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{{Coexpression_clusters
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|full_id=C2142_corpus_optic_Retinal_substantia_thalamus_globus_medulla
|id=C2142
}}

Latest revision as of 11:59, 17 September 2013


Full id: C2142_corpus_optic_Retinal_substantia_thalamus_globus_medulla



Phase1 CAGE Peaks

Hg19::chr11:61520075..61520136,+p1@C11orf9
Hg19::chr11:61533546..61533565,+p@chr11:61533546..61533565
+
Hg19::chr11:61537749..61537776,-p@chr11:61537749..61537776
-
Hg19::chr11:61539002..61539027,-p@chr11:61539002..61539027
-


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
mesothelial cell1.61e-0819
Uber Anatomy
Ontology termp-valuen
neural tube2.54e-2656
neural rod2.54e-2656
future spinal cord2.54e-2656
neural keel2.54e-2656
neural plate5.66e-2482
presumptive neural plate5.66e-2482
regional part of nervous system1.23e-2353
regional part of brain1.23e-2353
neurectoderm2.21e-2386
brain6.25e-2368
future brain6.25e-2368
tube5.04e-22192
central nervous system1.89e-2181
nervous system4.42e-2189
brain grey matter2.10e-1934
gray matter2.10e-1934
telencephalon3.24e-1934
regional part of forebrain1.33e-1841
forebrain1.33e-1841
anterior neural tube1.33e-1841
future forebrain1.33e-1841
pre-chordal neural plate5.94e-1861
regional part of telencephalon1.42e-1732
cerebral hemisphere2.51e-1732
adult organism6.44e-17114
cell layer3.15e-15309
structure with developmental contribution from neural crest4.41e-15132
epithelium6.85e-15306
multi-tissue structure1.85e-14342
ecto-epithelium1.89e-14104
organ system subdivision2.07e-14223
anatomical conduit1.74e-13240
regional part of cerebral cortex3.30e-1222
anatomical cluster3.40e-12373
cerebral cortex6.67e-1225
pallium6.67e-1225
neocortex9.40e-1120
neural nucleus1.23e-099
nucleus of brain1.23e-099
sac2.36e-0926
epithelial sac4.86e-0925
posterior neural tube6.23e-0915
chordal neural plate6.23e-0915
basal ganglion6.50e-099
nuclear complex of neuraxis6.50e-099
aggregate regional part of brain6.50e-099
collection of basal ganglia6.50e-099
cerebral subcortex6.50e-099
organ part1.50e-08218
epithelium of foregut-midgut junction2.84e-0825
anatomical boundary2.84e-0825
hepatobiliary system2.84e-0825
foregut-midgut junction2.84e-0825
septum transversum2.84e-0825
abdomen element3.09e-0854
abdominal segment element3.09e-0854
digestive tract diverticulum5.28e-0823
hepatic diverticulum1.09e-0722
liver primordium1.09e-0722
telencephalic nucleus1.09e-077
ectoderm-derived structure1.34e-07171
ectoderm1.34e-07171
presumptive ectoderm1.34e-07171
segmental subdivision of nervous system3.57e-0713
duct4.57e-0719
brainstem7.66e-076


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)
MA0003.12.39007
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
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
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.11.47051
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.17.60032
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.11.32557
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
MA0114.11.13665
MA0115.11.45393
MA0116.12.9994
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
MA0145.11.08195
MA0146.11.75643
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
MA0104.21.01696
MA0047.20.856092
MA0112.21.05083
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.88496
MA0155.13.05999
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.13.83423
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.23.5408
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
CTCF#1066445.360256373075030.001211145381643620.00815806594733817



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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