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Coexpression cluster:C4260: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4260_pineal_globus_thalamus_occipital_corpus_middle_extraskeletal
|id=C4260
}}

Latest revision as of 12:42, 17 September 2013


Full id: C4260_pineal_globus_thalamus_occipital_corpus_middle_extraskeletal



Phase1 CAGE Peaks

Hg19::chr3:106959530..106959548,+p1@LOC344595
Hg19::chr3:106959552..106959576,+p1@ENST00000473550
Hg19::chr3:106959578..106959602,+p2@ENST00000473550


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
fibroblast8.41e-0876
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure2.79e-35171
ectoderm2.79e-35171
presumptive ectoderm2.79e-35171
nervous system1.77e-3489
central nervous system2.54e-3481
brain5.34e-3368
future brain5.34e-3368
neural tube6.27e-3156
neural rod6.27e-3156
future spinal cord6.27e-3156
neural keel6.27e-3156
neural plate2.23e-3082
presumptive neural plate2.23e-3082
structure with developmental contribution from neural crest1.13e-29132
regional part of nervous system3.60e-2953
regional part of brain3.60e-2953
neurectoderm6.59e-2986
ecto-epithelium3.64e-28104
regional part of forebrain1.70e-2541
forebrain1.70e-2541
anterior neural tube1.70e-2541
future forebrain1.70e-2541
pre-chordal neural plate3.07e-2461
organ system subdivision4.00e-22223
adult organism4.77e-22114
multi-tissue structure1.26e-21342
telencephalon1.87e-2134
brain grey matter2.31e-2134
gray matter2.31e-2134
anatomical cluster7.42e-21373
regional part of telencephalon3.93e-2032
cerebral hemisphere4.38e-2032
cerebral cortex1.03e-1525
pallium1.03e-1525
epithelium2.23e-15306
cell layer3.07e-15309
regional part of cerebral cortex6.62e-1522
multi-cellular organism2.19e-14656
neocortex8.72e-1420
organ part7.07e-12218
anatomical system1.21e-11624
embryonic structure1.66e-11564
anatomical group1.83e-11625
anatomical conduit4.31e-11240
germ layer1.11e-10560
germ layer / neural crest1.11e-10560
embryonic tissue1.11e-10560
presumptive structure1.11e-10560
germ layer / neural crest derived structure1.11e-10560
epiblast (generic)1.11e-10560
developing anatomical structure1.81e-10581
embryo1.10e-09592
tube3.10e-08192
organ1.03e-07503
neural nucleus4.04e-079
nucleus of brain4.04e-079
basal ganglion4.15e-079
nuclear complex of neuraxis4.15e-079
aggregate regional part of brain4.15e-079
collection of basal ganglia4.15e-079
cerebral subcortex4.15e-079
posterior neural tube8.01e-0715
chordal neural plate8.01e-0715


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.12.61424
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.12.15449
MA0076.10.734647
MA0077.11.28751
MA0078.12.37746
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0145.10.273764
MA0146.10.348055
MA0147.14.68342
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.25.45805
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.11.76247
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
E2F1#186934.907389214879320.008460985347239390.0326458123496503
E2F6#187635.017155731697390.00791769806886330.0323304714631901
EGR1#195834.988179094810140.008056488137383440.0321579042453732
MXI1#460139.96157162875930.001011470541259020.00721564015427261
MYC#460935.22228187160940.007020843755740150.0295319948852449
NRF1#4899312.21027944771090.0005492172401020010.00472290649147904



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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