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Coexpression cluster:C4657: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4657_corpus_globus_optic_thalamus_medulla_locus_substantia
|id=C4657
}}

Latest revision as of 14:17, 17 September 2013


Full id: C4657_corpus_globus_optic_thalamus_medulla_locus_substantia



Phase1 CAGE Peaks

Hg19::chr7:139477500..139477580,-p2@HIPK2
Hg19::chr7:139477785..139477853,-p1@HIPK2
Hg19::chr7:139477913..139477929,-p3@HIPK2


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
classical monocyte8.17e-1042
CD14-positive, CD16-negative classical monocyte8.17e-1042
defensive cell1.20e-0748
phagocyte1.20e-0748
myeloid leukocyte2.60e-0772
Uber Anatomy
Ontology termp-valuen
adult organism3.20e-36114
neural tube9.33e-2756
neural rod9.33e-2756
future spinal cord9.33e-2756
neural keel9.33e-2756
regional part of nervous system7.28e-2553
regional part of brain7.28e-2553
neural plate7.14e-2382
presumptive neural plate7.14e-2382
brain1.48e-2268
future brain1.48e-2268
central nervous system1.14e-2181
regional part of forebrain1.98e-2141
forebrain1.98e-2141
anterior neural tube1.98e-2141
future forebrain1.98e-2141
nervous system1.17e-1989
neurectoderm1.20e-1986
brain grey matter9.43e-1834
gray matter9.43e-1834
telencephalon1.06e-1734
pre-chordal neural plate1.16e-1761
regional part of telencephalon1.90e-1632
cerebral hemisphere2.29e-1632
ecto-epithelium6.51e-16104
structure with developmental contribution from neural crest1.01e-15132
organ2.67e-15503
anatomical group5.19e-14625
anatomical system1.30e-13624
anatomical conduit3.54e-13240
organ system subdivision4.36e-13223
embryo7.59e-13592
developing anatomical structure1.68e-12581
regional part of cerebral cortex3.39e-1222
cerebral cortex3.82e-1225
pallium3.82e-1225
tube5.09e-12192
ectoderm-derived structure1.01e-11171
ectoderm1.01e-11171
presumptive ectoderm1.01e-11171
germ layer1.59e-11560
germ layer / neural crest1.59e-11560
embryonic tissue1.59e-11560
presumptive structure1.59e-11560
germ layer / neural crest derived structure1.59e-11560
epiblast (generic)1.59e-11560
neocortex4.82e-1120
anatomical cluster6.48e-11373
embryonic structure6.91e-11564
epithelium1.29e-10306
multi-cellular organism1.57e-10656
cell layer2.23e-10309
multi-tissue structure4.73e-10342
tissue1.31e-08773
neural nucleus3.00e-079
nucleus of brain3.00e-079
basal ganglion4.60e-079
nuclear complex of neuraxis4.60e-079
aggregate regional part of brain4.60e-079
collection of basal ganglia4.60e-079
cerebral subcortex4.60e-079


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)
MA0003.17.68548
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.17.37849
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.15.1975
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.13.00132
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.16.1256
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.210.8725
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
EGR1#195834.988179094810140.008056488137383440.0322392261994785
ELF1#199734.258097958807540.01295179875054610.0464836051446145
HMGN3#932438.178547723350590.001827766942164210.0109173664096476
NR2C2#7182332.61461090524092.88098172333076e-050.000606382205165138
NR3C1#2908314.9730233311730.0002978331194675480.00310154483638162
REST#597839.650028716128020.001112636247114590.00771085713420044
SRF#6722313.79717826216780.0003806615025800190.00376369465757404
YY1#752834.911170749853860.008441455341808260.0331148688894232
ZBTB7A#5134137.35190930787590.002516255860282270.0140886316298729



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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