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Coexpression cluster:C2714: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2714_salivary_dura_skin_trachea_rectum_skeletal_spinal
|id=C2714
|ontology_enrichment_celltype=CL:0000055!8.84e-10!180;CL:0000133!3.86e-09!59;CL:0000221!2.78e-08!71
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.83e-28!115;UBERON:0000924!1.07e-27!173;UBERON:0006601!1.07e-27!173;UBERON:0004121!3.66e-27!169;UBERON:0005743!1.33e-26!86;UBERON:0001017!1.75e-26!82;UBERON:0000073!8.68e-26!94;UBERON:0001016!8.68e-26!94;UBERON:0000475!4.38e-24!365;UBERON:0001049!1.48e-23!57;UBERON:0005068!1.48e-23!57;UBERON:0006241!1.48e-23!57;UBERON:0007135!1.48e-23!57;UBERON:0000033!2.69e-23!123;UBERON:0000153!2.86e-23!129;UBERON:0007811!2.86e-23!129;UBERON:0002346!3.93e-23!90;UBERON:0003075!8.52e-23!86;UBERON:0007284!8.52e-23!86;UBERON:0000955!3.65e-22!69;UBERON:0006238!3.65e-22!69;UBERON:0002616!7.21e-22!59;UBERON:0000481!4.44e-16!347;UBERON:0003080!6.80e-16!42;UBERON:0002780!2.52e-15!41;UBERON:0001890!2.52e-15!41;UBERON:0006240!2.52e-15!41;UBERON:0003056!4.76e-15!61;UBERON:0000468!1.87e-14!659;UBERON:0002020!5.17e-13!34;UBERON:0003528!5.17e-13!34;UBERON:0001893!2.64e-12!34;UBERON:0002791!2.92e-12!33;UBERON:0000062!4.50e-12!511;UBERON:0000064!1.54e-11!219;UBERON:0001869!1.64e-11!32;UBERON:0000922!1.38e-10!612;UBERON:0000119!5.50e-10!312;UBERON:0000956!9.44e-10!25;UBERON:0000203!9.44e-10!25;UBERON:0000483!1.30e-09!309;UBERON:0000477!1.68e-09!286;UBERON:0000467!3.04e-09!625;UBERON:0003076!4.77e-09!15;UBERON:0003057!4.77e-09!15;UBERON:0000480!5.06e-09!626;UBERON:0002050!8.22e-09!605;UBERON:0005423!8.22e-09!605;UBERON:0000923!1.73e-08!604;UBERON:0005291!1.73e-08!604;UBERON:0006598!1.73e-08!604;UBERON:0002532!1.73e-08!604;UBERON:0004111!2.68e-08!241;UBERON:0002619!2.95e-08!22;UBERON:0003102!2.43e-07!95;UBERON:0001950!3.21e-07!20;UBERON:0004733!4.46e-07!12;UBERON:0002028!4.46e-07!12;UBERON:0007277!4.46e-07!12;UBERON:0004732!6.05e-07!13
}}

Latest revision as of 12:11, 17 September 2013


Full id: C2714_salivary_dura_skin_trachea_rectum_skeletal_spinal



Phase1 CAGE Peaks

Hg19::chr3:112930306..112930338,+p2@BOC
Hg19::chr3:112930339..112930363,+p4@BOC
Hg19::chr3:112930373..112930384,+p5@BOC
Hg19::chr3:112930387..112930431,+p1@BOC


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><br>

Cell Type
Ontology termp-valuen
neurectodermal cell5.59e-0959
ectodermal cell7.86e-0872
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure2.12e-27171
ectoderm2.12e-27171
presumptive ectoderm2.12e-27171
adult organism1.82e-26114
central nervous system4.74e-2681
nervous system5.57e-2589
neurectoderm1.72e-2386
neural tube2.80e-2356
neural rod2.80e-2356
future spinal cord2.80e-2356
neural keel2.80e-2356
neural plate7.98e-2382
presumptive neural plate7.98e-2382
structure with developmental contribution from neural crest5.53e-22132
brain1.06e-2168
future brain1.06e-2168
regional part of nervous system2.57e-2153
regional part of brain2.57e-2153
ecto-epithelium7.43e-20104
organ system subdivision8.07e-19223
multi-tissue structure8.21e-18342
anatomical cluster2.28e-16373
regional part of forebrain1.70e-1541
forebrain1.70e-1541
anterior neural tube1.70e-1541
future forebrain1.70e-1541
multi-cellular organism8.46e-15656
pre-chordal neural plate3.14e-1461
brain grey matter2.27e-1334
gray matter2.27e-1334
telencephalon9.81e-1334
regional part of telencephalon3.01e-1232
cerebral hemisphere5.98e-1232
organ7.16e-12503
organ part2.78e-11218
cerebral cortex4.66e-1025
pallium4.66e-1025
cell layer6.85e-10309
embryo8.46e-10592
anatomical system1.08e-09624
epithelium1.80e-09306
anatomical group1.82e-09625
posterior neural tube3.31e-0915
chordal neural plate3.31e-0915
regional part of cerebral cortex1.10e-0822
anatomical conduit3.09e-08240
embryonic structure3.25e-08564
developing anatomical structure3.60e-08581
germ layer7.50e-08560
germ layer / neural crest7.50e-08560
embryonic tissue7.50e-08560
presumptive structure7.50e-08560
germ layer / neural crest derived structure7.50e-08560
epiblast (generic)7.50e-08560
neocortex1.29e-0720
segmental subdivision of hindbrain3.00e-0712
hindbrain3.00e-0712
presumptive hindbrain3.00e-0712
surface structure5.54e-0799


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
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
MA0050.11.66718
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.11.98521
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.11.68681
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
MA0081.10.604638
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
MA0105.14.42006
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.12.9994
MA0117.11.24497
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.11.813
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.22.35208
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.11.84959
MA0153.11.30799
MA0154.11.88496
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.25.92758
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#186944.907389214879320.001724022357361790.0106648801149386
ZNF263#1012748.221841637010680.0002187871180958320.00249425912310999



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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