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Coexpression cluster:C3484: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3484_CD4_cerebellum_CD8_pineal_thalamus_substantia_optic
|id=C3484
}}

Latest revision as of 12:27, 17 September 2013


Full id: C3484_CD4_cerebellum_CD8_pineal_thalamus_substantia_optic



Phase1 CAGE Peaks

Hg19::chr15:40987282..40987311,-p1@LOC100505648
Hg19::chr21:34144448..34144480,+p1@C21orf49
Hg19::chr7:149535455..149535555,+p1@ZNF862


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>

Uber Anatomy
Ontology termp-valuen
adult organism2.15e-34114
neural tube6.18e-2456
neural rod6.18e-2456
future spinal cord6.18e-2456
neural keel6.18e-2456
regional part of nervous system2.01e-2253
regional part of brain2.01e-2253
nervous system4.59e-2089
brain9.59e-2068
future brain9.59e-2068
central nervous system2.04e-1981
regional part of forebrain1.97e-1841
forebrain1.97e-1841
anterior neural tube1.97e-1841
future forebrain1.97e-1841
neurectoderm2.18e-1886
neural plate1.35e-1782
presumptive neural plate1.35e-1782
telencephalon1.04e-1434
brain grey matter1.07e-1434
gray matter1.07e-1434
pre-chordal neural plate9.88e-1461
regional part of telencephalon1.31e-1332
cerebral hemisphere1.88e-1332
ecto-epithelium7.05e-11104
ectoderm-derived structure1.31e-10171
ectoderm1.31e-10171
presumptive ectoderm1.31e-10171
regional part of cerebral cortex1.88e-1022
cerebral cortex4.89e-1025
pallium4.89e-1025
neocortex1.20e-0920
structure with developmental contribution from neural crest2.29e-07132
posterior neural tube9.73e-0715
chordal neural plate9.73e-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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
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
MA0060.12.13518
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
MA0073.10.0185922
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
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
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
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
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.481578
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
BRCA1#672213.45615376214920.007119807716084560.0296178442627322
CHD2#1106310.34402283411690.0009033701102746880.00659539118818442
E2F1#186934.907389214879320.008460985347239390.0324492086031263
E2F4#1874312.66806031528440.0004917987006298980.00436351750021969
E2F6#187635.017155731697390.00791769806886330.0321369736354597
ELF1#199734.258097958807540.01295179875054610.0461175176335032
ETS1#211339.728760922202340.001085840092584840.00760947818757752
IRF1#365937.63716375356390.002244692747297240.012784025838967
MXI1#460139.96157162875930.001011470541259020.00719303907521115
MYC#460935.22228187160940.007020843755740150.0293911295897766
NRF1#4899312.21027944771090.0005492172401020010.00470392810718492
POLR3A#111281113.0440366972480.00882009881003120.0334980290054493
SIN3A#2594235.408884726815140.006318961977991520.0276001033005502
SP1#666735.69838137814090.005403962701712170.0245994185853688
TFAP2A#7020211.01242291536330.01054990655215560.0390039183829722
USF1#739136.361499277207960.00388404057290560.0189944424702045
XRCC4#751811432.767441860460.0006977913838891460.00561237076180196
ZZZ3#26009179.80440414507770.0124784379082580.0451571578898321



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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