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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.0783999907478192,

Latest revision as of 12:10, 17 September 2013


Full id: C2681_amygdala_duodenum_insula_rhabdomyosarcoma_medial_frontal_brain



Phase1 CAGE Peaks

Hg19::chr2:204193085..204193096,+p3@ABI2
Hg19::chr2:204193101..204193128,+p2@ABI2
Hg19::chr2:204193129..204193139,+p4@ABI2
Hg19::chr2:204193149..204193156,+p5@ABI2


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>disease_data<br>

Cell Type
Ontology termp-valuen
neural cell1.43e-0925
neurectodermal cell8.75e-0759
Uber Anatomy
Ontology termp-valuen
nervous system8.16e-3789
central nervous system8.95e-3681
brain1.23e-2968
future brain1.23e-2968
neural tube2.16e-2956
neural rod2.16e-2956
future spinal cord2.16e-2956
neural keel2.16e-2956
regional part of nervous system5.59e-2853
regional part of brain5.59e-2853
neurectoderm8.92e-2886
neural plate1.90e-2682
presumptive neural plate1.90e-2682
regional part of forebrain1.65e-2241
forebrain1.65e-2241
anterior neural tube1.65e-2241
future forebrain1.65e-2241
ectoderm-derived structure3.75e-22171
ectoderm3.75e-22171
presumptive ectoderm3.75e-22171
pre-chordal neural plate5.82e-2261
anatomical cluster1.02e-21373
structure with developmental contribution from neural crest1.25e-21132
telencephalon4.89e-2034
brain grey matter7.39e-2034
gray matter7.39e-2034
cerebral hemisphere2.30e-1932
ecto-epithelium3.22e-19104
organ system subdivision3.66e-19223
regional part of telencephalon6.07e-1932
cerebral cortex1.16e-1525
pallium1.16e-1525
cell layer4.65e-15309
tube4.83e-15192
epithelium2.36e-14306
regional part of cerebral cortex3.92e-1422
multi-tissue structure2.61e-13342
neocortex6.15e-1320
anatomical conduit1.67e-12240
posterior neural tube4.96e-0815
chordal neural plate4.96e-0815
organ part2.58e-07218
Disease
Ontology termp-valuen
cancer3.48e-12235
cell type cancer4.65e-12143
disease of cellular proliferation5.34e-12239
germ cell and embryonal cancer1.89e-0722
germ cell cancer1.89e-0722
carcinoma4.83e-07106


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)
MA0003.13.49532
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.12.32784
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
MA0055.10.125954
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
MA0068.16.27432
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.10.819248
MA0076.12.5647
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
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
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.12.78257
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.12.47057
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.22.51225
MA0035.20.778873
MA0039.23.07509
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.22.43626
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.11.61785
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.14.24646
MA0163.12.49771
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.215.4083
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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#90546.336201576962630.0006203100587215640.00512901292239897
CHD2#1106410.34402283411698.73193255208051e-050.00129190296615206
E2F1#186944.907389214879320.001724022357361790.0106629853713436
EGR1#195844.988179094810140.001615011500076050.010155348669784
ELF1#199744.258097958807540.003041525565781240.0161122946266613
ELK4#2005416.2356816584681.43847748454449e-050.000343547107268104
EP300#203346.77394172622320.0004748459821442640.00434602046526727
FOXA1#3169411.08141974938556.62943068949433e-050.00107211383056689
GABPB1#255347.067683836182170.0004006876864423170.00390622806724065
HDAC2#3066413.41562023662633.0859005065161e-050.000627508494937763
HEY1#2346244.040111043105710.00375304636917980.0186374594527493
HMGN3#932448.178547723350590.0002234570284440470.00248378337523072
HNF4A#3172423.13229036295373.48990320893214e-060.000115745316366359
HNF4G#3174428.75342252644681.46167379934821e-065.67493494164044e-05
JUND#372746.994663941871030.000417684217818580.003920773146212
NANOG#79923429.24477848101271.36586687657858e-065.34468979853843e-05
NRF1#4899412.21027944771094.49717228915276e-050.000794586663351083
REST#597849.650028716128020.0001152825614219170.00157282762016246
RXRA#6256420.07461713913336.1537798808435e-060.000182480016177006
SIN3A#2594245.408884726815140.001168172384885160.00797299409913873
SP1#666745.69838137814090.0009482606065333980.00684986785763878
SREBF1#6720447.00584944048832.04523668136926e-071.1038887533102e-05
TAF1#687243.343046285745290.008005664898701650.0322757628394326
TBP#690843.706770687096390.005296377814784350.0244626040420247
YY1#752844.911170749853860.00171871838055440.0106966944131292
ZBTB33#10009431.66472502998129.93721537730495e-074.20175237566944e-05
ZBTB7A#5134147.35190930787590.000342223540015990.00347038394948344
ZNF143#7702413.50087655222793.00867915035614e-050.000621363341475272
ZNF263#1012748.221841637010680.0002187871180958320.00249398688352004



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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