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Coexpression cluster:C2739: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;6.84463,MA0004.1;0.71247,MA0006.1;2.26728,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;3.08565,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;1.92746,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;6.69514,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;8.53298,MA0056.1;0,MA0057.1;3.6449,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;2.70115,MA0061.1;0.946082,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;1.02755,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;2.66951,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;1.43218,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;4.40535,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;1.70272,MA0146.1;0.061409,MA0147.1;2.03364,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;5.64763,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;2.6968,MA0047.2;0.856092,MA0112.2;6.77569,MA0065.2;1.09513,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;1.61785,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;6.73484,MA0163.1;0.539587,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;13.9787,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;3.06353,MA0442.1;0
}}
}}

Revision as of 20:52, 22 January 2013


Full id: C2739_retina_cerebellum_Hepatocyte_salivary_submaxillary_parotid_small



Phase1 CAGE Peaks

Hg19::chr3:39851061..39851085,+p4@MYRIP
Hg19::chr3:39851094..39851151,+p1@MYRIP
Hg19::chr3:39851154..39851165,+p6@MYRIP
Hg19::chr3:39851170..39851195,+p3@MYRIP


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>

Uber Anatomy
Ontology termp-valuen
adult organism3.56e-59114
neural tube3.32e-3756
neural rod3.32e-3756
future spinal cord3.32e-3756
neural keel3.32e-3756
regional part of nervous system1.32e-3453
regional part of brain1.32e-3453
central nervous system7.73e-3381
nervous system1.23e-3289
regional part of forebrain9.19e-2941
forebrain9.19e-2941
anterior neural tube9.19e-2941
future forebrain9.19e-2941
brain1.54e-2668
future brain1.54e-2668
brain grey matter2.10e-2534
gray matter2.10e-2534
neural plate2.16e-2582
presumptive neural plate2.16e-2582
telencephalon2.74e-2534
anatomical cluster1.89e-24373
cerebral hemisphere1.02e-2332
regional part of telencephalon1.65e-2332
neurectoderm3.19e-2386
tube1.17e-22192
anatomical conduit1.59e-22240
regional part of cerebral cortex4.74e-2222
organ system subdivision5.86e-22223
neocortex2.53e-2020
pre-chordal neural plate9.76e-1961
cerebral cortex2.25e-1825
pallium2.25e-1825
ecto-epithelium6.41e-18104
structure with developmental contribution from neural crest3.05e-16132
ectoderm-derived structure1.33e-13171
ectoderm1.33e-13171
presumptive ectoderm1.33e-13171
epithelium6.74e-12306
cell layer1.80e-11309
blood vessel endothelium3.74e-1018
endothelium3.74e-1018
cardiovascular system endothelium3.74e-1018
posterior neural tube1.73e-0915
chordal neural plate1.73e-0915
multi-cellular organism6.66e-09656
anatomical system1.13e-08624
anatomical group1.41e-08625
embryo1.66e-08592
neural nucleus1.70e-089
nucleus of brain1.70e-089
germ layer2.79e-08560
germ layer / neural crest2.79e-08560
embryonic tissue2.79e-08560
presumptive structure2.79e-08560
germ layer / neural crest derived structure2.79e-08560
epiblast (generic)2.79e-08560
embryonic structure2.88e-08564
basal ganglion3.14e-089
nuclear complex of neuraxis3.14e-089
aggregate regional part of brain3.14e-089
collection of basal ganglia3.14e-089
cerebral subcortex3.14e-089
segmental subdivision of nervous system6.14e-0813
developing anatomical structure1.19e-07581
multi-tissue structure1.39e-07342
temporal lobe1.94e-076
simple squamous epithelium2.14e-0722
brainstem2.19e-076
gyrus2.39e-076
segmental subdivision of hindbrain4.01e-0712
hindbrain4.01e-0712
presumptive hindbrain4.01e-0712


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)
MA0003.16.84463
MA0004.10.71247
MA0006.12.26728
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
MA0038.11.92746
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.16.69514
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.18.53298
MA0056.10
MA0057.13.6449
MA0058.10.605914
MA0059.10.604454
MA0060.12.70115
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
MA0073.10.00636811
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
MA0105.12.66951
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.11.43218
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.14.40535
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.70272
MA0146.10.061409
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.25.64763
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.22.6968
MA0047.20.856092
MA0112.26.77569
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.16.73484
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.213.9787
MA0102.21.75932
MA0258.10.418966
MA0259.13.06353
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#90546.336201576962630.0006203100587215640.00513104405376378
CTCF#1066445.360256373075030.001211145381643620.00818763755022838
E2F1#186944.907389214879320.001724022357361790.0106667755320206
E2F6#187645.017155731697390.00157802193473060.00998285982441874
EGR1#195844.988179094810140.001615011500076050.0101584067728525
NFYA#4800418.42558069983058.67100748407158e-060.000234852528690081
NFYB#4801416.75979325353651.26678572070404e-050.000311665097490246
RAD21#5885410.35503389545638.6948481184721e-050.00129725891806444



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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