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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.132361521956367,

Latest revision as of 12:01, 17 September 2013


Full id: C2241_cerebellum_spinal_thalamus_medulla_substantia_occipital_hippocampus



Phase1 CAGE Peaks

Hg19::chr12:75784669..75784698,-p1@CAPS2
Hg19::chr19:44455368..44455396,+p1@ZNF221
Hg19::chr1:144932014..144932132,-p3@PDE4DIP
Hg19::chr9:95640300..95640345,-p1@ZNF484


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 organism6.62e-37114
nervous system7.04e-3289
central nervous system1.28e-3181
neural tube2.66e-2956
neural rod2.66e-2956
future spinal cord2.66e-2956
neural keel2.66e-2956
regional part of nervous system2.24e-2753
regional part of brain2.24e-2753
brain3.34e-2668
future brain3.34e-2668
regional part of forebrain3.95e-2541
forebrain3.95e-2541
anterior neural tube3.95e-2541
future forebrain3.95e-2541
ectoderm-derived structure2.03e-22171
ectoderm2.03e-22171
presumptive ectoderm2.03e-22171
neural plate4.70e-2282
presumptive neural plate4.70e-2282
neurectoderm2.51e-2186
brain grey matter9.40e-2134
gray matter9.40e-2134
telencephalon1.07e-2034
regional part of telencephalon1.74e-1932
cerebral hemisphere2.00e-1932
organ system subdivision1.50e-17223
pre-chordal neural plate1.48e-1661
ecto-epithelium2.94e-16104
structure with developmental contribution from neural crest1.95e-15132
cerebral cortex3.05e-1525
pallium3.05e-1525
regional part of cerebral cortex2.53e-1422
neocortex3.87e-1320
anatomical cluster4.74e-07373
basal ganglion5.40e-079
nuclear complex of neuraxis5.40e-079
aggregate regional part of brain5.40e-079
collection of basal ganglia5.40e-079
cerebral subcortex5.40e-079
neural nucleus5.47e-079
nucleus of brain5.47e-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)
MA0003.10.233555
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.11.98521
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.12.44319
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.22.35208
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.11.02191
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.21.11128
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
ELF1#199744.258097958807540.003041525565781240.0160666576584202
ETS1#211337.296570691651750.00400857377511390.0192006712758724
GABPB1#255335.300762877136630.01012678824234270.0378455463122462
MAFF#23764228.15767824497260.001846876180367150.0109234285537074
MAFK#7975213.5503665689150.00777202812098050.0319505154468444
MAX#414934.839416631755340.01315737137836840.0466032255777458
NANOG#79923214.62238924050630.006698757715363760.0284823334704586
NFKB1#479045.488063424193840.001102199566301980.00767059508929248
NRF1#489939.157709585783180.002061953791733420.0119598129542845
PBX3#5090210.95725634337210.01174530180688030.0428260857943922
RAD21#588537.766275421592250.0033411193858720.0172633041874579
SETDB1#9869220.16001308900520.00356908685407640.0180824615287128
SIX5#147912312.81503651659420.0007664471136930380.00601404734087057
SMC3#9126311.28369963369960.001115802366868050.00765558293215956
STAT1#6772315.52994062289940.000434088655175550.00404964582919868
STAT3#6774410.51946499715428.16377768286615e-050.00122961750421237
TAF1#687243.343046285745290.008005664898701650.032150412841479
TBP#690843.706770687096390.005296377814784350.0243699181689251
TRIM28#10155418.59052504526258.36730015875654e-060.000229785027946457
YY1#752844.911170749853860.00171871838055440.0106674528404779
ZNF143#7702413.50087655222793.00867915035614e-050.000620137047136461
ZNF263#1012748.221841637010680.0002187871180958320.00248179730930929



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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