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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 12:38, 17 September 2013


Full id: C4063_alveolar_medial_occipital_brain_olfactory_amygdala_hippocampus



Phase1 CAGE Peaks

Hg19::chr20:62284737..62284748,-p3@STMN3
Hg19::chr20:62284766..62284785,-p1@STMN3
Hg19::chr20:62284790..62284807,-p2@STMN3


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
nervous system7.56e-3189
neurectoderm8.02e-3186
central nervous system1.69e-3081
neural plate4.48e-2982
presumptive neural plate4.48e-2982
neural tube3.18e-2756
neural rod3.18e-2756
future spinal cord3.18e-2756
neural keel3.18e-2756
regional part of nervous system4.32e-2653
regional part of brain4.32e-2653
brain3.43e-2568
future brain3.43e-2568
pre-chordal neural plate1.21e-2161
ecto-epithelium1.34e-21104
ectoderm-derived structure3.15e-20171
ectoderm3.15e-20171
presumptive ectoderm3.15e-20171
regional part of forebrain3.67e-2041
forebrain3.67e-2041
anterior neural tube3.67e-2041
future forebrain3.67e-2041
structure with developmental contribution from neural crest1.06e-19132
brain grey matter1.91e-1834
gray matter1.91e-1834
cerebral hemisphere3.57e-1832
telencephalon4.06e-1834
regional part of telencephalon2.75e-1732
regional part of cerebral cortex9.44e-1522
cerebral cortex2.36e-1425
pallium2.36e-1425
neocortex1.58e-1320
cell layer4.37e-13309
adult organism7.63e-13114
epithelium2.75e-12306
organ system subdivision9.05e-12223
anatomical cluster5.13e-11373
tube9.50e-11192
multi-tissue structure2.29e-09342
organ part5.03e-09218
posterior neural tube3.23e-0815
chordal neural plate3.23e-0815
segmental subdivision of nervous system1.42e-0713
segmental subdivision of hindbrain3.50e-0712
hindbrain3.50e-0712
presumptive hindbrain3.50e-0712
anatomical conduit6.91e-07240


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
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
MA0055.12.37507
MA0056.10
MA0057.13.3282
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
MA0073.11.36698
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.13.60951
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
MA0145.11.37817
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.127.0439
MA0062.22.96208
MA0035.20.894194
MA0039.20.757898
MA0138.23.88672
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
MA0162.13.52399
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.224.7816
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
CCNT2#90536.336201576962630.003930750035764890.0190330382950183
E2F4#1874312.66806031528440.0004917987006298980.00437764974815358
E2F6#187635.017155731697390.00791769806886330.0322875509981654
EGR1#195834.988179094810140.008056488137383440.0321173969226731
ELF1#199734.258097958807540.01295179875054610.0463085556216461
ELK4#2005316.2356816584680.0002336043955745990.00255925831001946
ETS1#211339.728760922202340.001085840092584840.00763355233100887
FOSL2#2355316.93020060456170.0002060162053171620.00243367565514298
GABPB1#255337.067683836182170.002832212825417420.0154356559658597
HDAC2#3066313.41562023662630.0004140761399857210.00391789255154636
HMGN3#932438.178547723350590.001827766942164210.0108856154010429
IRF1#365937.63716375356390.002244692747297240.0128295006750384
MAX#414936.452555509007120.003721913834265510.0186854280121547
MXI1#460139.96157162875930.001011470541259020.00721022263726374
MYC#460935.22228187160940.007020843755740150.0294975420792399
RAD21#5885310.35503389545630.0009004912073565420.00665061885334204
REST#597839.650028716128020.001112636247114590.0076879005631757
SIN3A#2594235.408884726815140.006318961977991520.027724166947549
SMARCB1#6598318.25271578115740.000164397760679890.00203382346927826
TAF7#6879311.43306940492390.0006690181981945830.00544001803186266
TCF7L2#6934310.77017656313730.0008003181298398380.00614681755863678
USF1#739136.361499277207960.00388404057290560.0190613840230106
YY1#752834.911170749853860.008441455341808260.0329860124384747
ZBTB7A#5134137.35190930787590.002516255860282270.0140464613711059
ZNF143#7702313.50087655222790.0004062804962997170.00389673328616458



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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