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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 12:03, 17 September 2013


Full id: C2314_salivary_pituitary_cerebellum_breast_small_occipital_brain



Phase1 CAGE Peaks

Hg19::chr14:77648077..77648103,+p3@TMEM63C
Hg19::chr14:77648123..77648162,+p1@TMEM63C
Hg19::chr14:77648167..77648183,+p2@TMEM63C
Hg19::chr14:77648188..77648205,+p4@TMEM63C


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
neural tube2.57e-3656
neural rod2.57e-3656
future spinal cord2.57e-3656
neural keel2.57e-3656
regional part of nervous system1.35e-3453
regional part of brain1.35e-3453
central nervous system1.90e-3481
brain3.01e-3368
future brain3.01e-3368
nervous system4.88e-3389
regional part of forebrain5.01e-3141
forebrain5.01e-3141
anterior neural tube5.01e-3141
future forebrain5.01e-3141
neural plate4.83e-2782
presumptive neural plate4.83e-2782
telencephalon1.55e-2534
brain grey matter1.88e-2534
gray matter1.88e-2534
neurectoderm2.05e-2586
pre-chordal neural plate2.89e-2561
ecto-epithelium8.64e-25104
cerebral hemisphere2.16e-2432
regional part of telencephalon4.67e-2432
ectoderm-derived structure1.53e-22171
ectoderm1.53e-22171
presumptive ectoderm1.53e-22171
adult organism7.99e-22114
organ system subdivision9.50e-21223
regional part of cerebral cortex5.28e-2022
cerebral cortex3.87e-1925
pallium3.87e-1925
neocortex5.48e-1920
structure with developmental contribution from neural crest2.13e-13132
organ part2.06e-09218
basal ganglion8.61e-089
nuclear complex of neuraxis8.61e-089
aggregate regional part of brain8.61e-089
collection of basal ganglia8.61e-089
cerebral subcortex8.61e-089
neural nucleus9.60e-089
nucleus of brain9.60e-089
organ1.86e-07503
temporal lobe4.71e-076
embryo5.90e-07592
posterior neural tube6.25e-0715
chordal neural plate6.25e-0715
diencephalon7.03e-077
future diencephalon7.03e-077
anatomical cluster9.03e-07373


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)
MA0003.11.45381
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.13.08565
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
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
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.12.9994
MA0117.11.24497
MA0119.14.80079
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.16.90001
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.777367
MA0138.22.1393
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.13.02177
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.122011
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
E2F1#186944.907389214879320.001724022357361790.0106365294766368
EBF1#187948.9064668465690.00015887907472010.00199461133365699
MYC#460945.22228187160940.001344309395272740.00886632958212121
SIN3A#2594245.408884726815140.001168172384885160.00795220673347809
SP1#666745.69838137814090.0009482606065333980.00683474047520646
STAT1#6772420.70658749719925.43610708103893e-060.000165041159138554
SUZ12#23512450.11578091106291.5827390373096e-078.79253629348818e-06
TAF1#687243.343046285745290.008005664898701650.0321677299305749
TRIM28#10155418.59052504526258.36730015875654e-060.000229905935617042
YY1#752844.911170749853860.00171871838055440.0106693550253638
ZEB1#6935416.88843201754391.22862303393937e-050.000303850724701857
ZNF263#1012748.221841637010680.0002187871180958320.00248314581904049



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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