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{{Coexpression_clusters
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|full_id=C4070_placenta_spinal_left_skeletal_lung_Skeletal_colon
|id=C4070
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.16e-46!115;UBERON:0000073!1.18e-31!94;UBERON:0001016!1.18e-31!94;UBERON:0001017!9.59e-31!82;UBERON:0005743!2.82e-30!86;UBERON:0001049!1.94e-28!57;UBERON:0005068!1.94e-28!57;UBERON:0006241!1.94e-28!57;UBERON:0007135!1.94e-28!57;UBERON:0003075!4.18e-28!86;UBERON:0007284!4.18e-28!86;UBERON:0002346!5.22e-26!90;UBERON:0000955!8.09e-25!69;UBERON:0006238!8.09e-25!69;UBERON:0002616!4.87e-24!59;UBERON:0004121!6.09e-22!169;UBERON:0003080!4.74e-21!42;UBERON:0000924!7.15e-21!173;UBERON:0006601!7.15e-21!173;UBERON:0002780!1.44e-20!41;UBERON:0001890!1.44e-20!41;UBERON:0006240!1.44e-20!41;UBERON:0000153!9.05e-20!129;UBERON:0007811!9.05e-20!129;UBERON:0003056!1.10e-19!61;UBERON:0000033!2.18e-19!123;UBERON:0001893!2.52e-17!34;UBERON:0002020!2.80e-17!34;UBERON:0003528!2.80e-17!34;UBERON:0002791!8.46e-17!33;UBERON:0001869!2.50e-16!32;UBERON:0000475!1.71e-13!365;UBERON:0000956!4.21e-13!25;UBERON:0000203!4.21e-13!25;UBERON:0002619!6.43e-12!22;UBERON:0001950!4.74e-11!20;UBERON:0000481!6.26e-09!347;UBERON:0003076!1.63e-08!15;UBERON:0003057!1.63e-08!15;UBERON:0000468!3.51e-08!659;UBERON:0000119!8.40e-08!312;UBERON:0000483!1.43e-07!309;UBERON:0000064!1.73e-07!219;UBERON:0004111!2.30e-07!241;UBERON:0000025!2.60e-07!194;UBERON:0004732!2.79e-07!13;UBERON:0000477!5.83e-07!286;UBERON:0000479!5.94e-07!787;UBERON:0004733!9.90e-07!12;UBERON:0002028!9.90e-07!12;UBERON:0007277!9.90e-07!12
}}

Latest revision as of 12:38, 17 September 2013


Full id: C4070_placenta_spinal_left_skeletal_lung_Skeletal_colon



Phase1 CAGE Peaks

Hg19::chr21:27011975..27012064,+p1@JAM2
Hg19::chr21:27012071..27012091,+p9@JAM2
Hg19::chr21:27012101..27012112,+p12@JAM2


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><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.82e-56114
nervous system1.11e-3489
central nervous system5.91e-3481
neural tube8.14e-3456
neural rod8.14e-3456
future spinal cord8.14e-3456
neural keel8.14e-3456
neural plate7.16e-3382
presumptive neural plate7.16e-3382
regional part of nervous system3.24e-3153
regional part of brain3.24e-3153
neurectoderm3.80e-3086
brain9.41e-2868
future brain9.41e-2868
regional part of forebrain1.83e-2641
forebrain1.83e-2641
anterior neural tube1.83e-2641
future forebrain1.83e-2641
structure with developmental contribution from neural crest1.91e-24132
pre-chordal neural plate9.78e-2461
ecto-epithelium5.82e-23104
ectoderm-derived structure8.39e-23171
ectoderm8.39e-23171
presumptive ectoderm8.39e-23171
telencephalon2.18e-2134
brain grey matter3.48e-2134
gray matter3.48e-2134
cerebral hemisphere3.75e-2032
regional part of telencephalon6.55e-2032
organ system subdivision2.06e-19223
cerebral cortex9.99e-1625
pallium9.99e-1625
regional part of cerebral cortex4.37e-1422
anatomical cluster5.75e-14373
neocortex9.22e-1320
organ part4.97e-12218
multi-tissue structure5.22e-10342
posterior neural tube1.74e-0815
chordal neural plate1.74e-0815
multi-cellular organism1.61e-07656
anatomical conduit2.00e-07240
tube3.31e-07192
neural nucleus6.37e-079
nucleus of brain6.37e-079
basal ganglion6.74e-079
nuclear complex of neuraxis6.74e-079
aggregate regional part of brain6.74e-079
collection of basal ganglia6.74e-079
cerebral subcortex6.74e-079
segmental subdivision of nervous system7.37e-0713


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)
MA0003.12.61626
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.12.76432
MA0019.10.990656
MA0024.12.72668
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
MA0055.18.91714
MA0056.10
MA0057.13.3282
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.14.06645
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.110.4901
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.11.84783
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.12.63873
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.12.34614
MA0108.21.15387
MA0109.10
MA0111.11.80901
MA0113.11.00436
MA0114.12.32521
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
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.12.37721
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.70224
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
CTCF#1066435.360256373075030.0064925092527670.0279951766586736
EBF1#187938.9064668465690.00141523283560980.00916282326689308
EGR1#195834.988179094810140.008056488137383440.0321186229178986
ELF1#199734.258097958807540.01295179875054610.0463117265717709
NFKB1#479035.488063424193840.006049381815655430.0269961708945536
RAD21#5885310.35503389545630.0009004912073565420.00665250061576783
SMC3#9126315.04493284493280.0002935825420371870.00309617965342035
YY1#752834.911170749853860.008441455341808260.0329897154034992



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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