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Coexpression cluster:C2143: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.0938548,MA0004.1;1.69588,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.524262,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;3.41834,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;1.28887,MA0056.1;0,MA0057.1;0.248209,MA0058.1;1.47358,MA0059.1;0.604454,MA0060.1;1.01899,MA0061.1;0.360128,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;0.599068,MA0074.1;0.819248,MA0076.1;2.5647,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;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;1.32557,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,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;2.01976,MA0117.1;1.24497,MA0119.1;0.586221,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;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.569905,MA0146.1;0.481,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;2.51225,MA0035.2;0.778873,MA0039.2;0.483275,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.649108,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.640035,MA0163.1;0.539587,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.122011,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;1.1888,MA0442.1;0
}}
}}

Revision as of 20:26, 22 January 2013


Full id: C2143_Mesenchymal_Alveolar_Osteoblast_Renal_Adipocyte_Placental_Fibroblast



Phase1 CAGE Peaks

Hg19::chr11:61560053..61560091,-p1@C11orf10
Hg19::chr17:7307407..7307424,-p1@C17orf61
p1@PLSCR3
Hg19::chr19:5903739..5903809,-p1@FUT5
p1@NDUFA11
Hg19::chr2:113342163..113342210,+p1@CHCHD5


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

GO IDGO nameFDR corrected p-value
GO:00170603-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity0.0082879592865696
GO:0046920alpha(1,3)-fucosyltransferase activity0.0082879592865696
GO:0019317fucose catabolic process0.0082879592865696
GO:0042355L-fucose catabolic process0.0082879592865696
GO:0042354L-fucose metabolic process0.0082879592865696
GO:0006004fucose metabolic process0.00941758099038374
GO:0008417fucosyltransferase activity0.00968622692758105
GO:0019320hexose catabolic process0.0480923729825549
GO:0046365monosaccharide catabolic process0.0480923729825549
GO:0046164alcohol catabolic process0.0480923729825549
GO:0006486protein amino acid glycosylation0.0480923729825549
GO:0043413biopolymer glycosylation0.0480923729825549
GO:0009101glycoprotein biosynthetic process0.0480923729825549
GO:0044275cellular carbohydrate catabolic process0.0480923729825549
GO:0016052carbohydrate catabolic process0.0480923729825549
GO:0009100glycoprotein metabolic process0.0488322814096535



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
epithelial vesicle1.13e-1978
somite2.19e-1671
presomitic mesoderm2.19e-1671
presumptive segmental plate2.19e-1671
dermomyotome2.19e-1671
trunk paraxial mesoderm2.19e-1671
dense mesenchyme tissue2.40e-1673
paraxial mesoderm6.58e-1672
presumptive paraxial mesoderm6.58e-1672
multilaminar epithelium1.04e-1583
skeletal muscle tissue3.65e-1462
striated muscle tissue3.65e-1462
myotome3.65e-1462
mesenchyme3.92e-14160
entire embryonic mesenchyme3.92e-14160
trunk mesenchyme1.81e-13122
muscle tissue3.42e-1364
musculature3.42e-1364
musculature of body3.42e-1364
unilaminar epithelium6.26e-13148
epithelial tube9.47e-11117
trunk9.58e-11199
organism subdivision1.87e-10264
vasculature1.99e-0978
vascular system1.99e-0978
splanchnic layer of lateral plate mesoderm3.61e-0883
vessel5.29e-0868
artery1.59e-0742
arterial blood vessel1.59e-0742
arterial system1.59e-0742
epithelial tube open at both ends2.07e-0759
blood vessel2.07e-0759
blood vasculature2.07e-0759
vascular cord2.07e-0759
cell layer9.09e-07309
epithelium9.19e-07306


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)
MA0003.10.0938548
MA0004.11.69588
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.13.41834
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.10.604454
MA0060.11.01899
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
MA0073.10.599068
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
MA0093.11.32557
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.12.01976
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
MA0145.10.569905
MA0146.10.481
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.22.51225
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.122011
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
ATF3#467211.23158726300440.01119559039922220.0411188727565187
CHD2#110637.758017125587640.003351522464536340.0172888301231706
E2F1#186944.907389214879320.001724022357361790.0106258584231636
ELF1#199744.258097958807540.003041525565781240.0160544773357236
ETS1#211337.296570691651750.00400857377511390.0191962692695273
HEY1#2346244.040111043105710.00375304636917980.01855540663467
MXI1#460137.471178721569470.003741314738550960.0186208144290661
NANOG#79923214.62238924050630.006698757715363760.0284800145342917
NRF1#4899412.21027944771094.49717228915276e-050.00079190722762911
PAX5#507935.002174148383370.01196533174786410.0434705284869787
POU2F2#545249.106124057742520.000145395665174930.00188072552330994
SIN3A#2594245.408884726815140.001168172384885160.00794340488996815
SREBF1#6720223.50292472024410.002638454900768240.0145805381968006
SRF#6722310.34788369662590.001439893778401260.0092354643691242
TAF1#687243.343046285745290.008005664898701650.0321257064610582
TAF7#6879411.43306940492395.85061525419808e-050.00096743572915325
TBP#690843.706770687096390.005296377814784350.024349535704462
USF1#739134.771124457905970.01370465887188020.0482732164559964
YY1#752844.911170749853860.00171871838055440.0106611171198385
ZBTB33#10009215.83236251499060.005734248930324640.025833803124587



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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