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Coexpression cluster:C2173: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,1.02453,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,1.18793,0.356737,0.223552,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.285913,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,1.63146,0.53106,0.0946706,0.61613,0.822818,0.694903,0.99221,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.823598,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,1.66879,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,1.28386,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,2.52313,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,1.41398,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,0.175846,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;1.31813,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.244769,MA0017.1;1.41335,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;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;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;4.32878,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.380957,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;0.182167,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;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;2.95284,MA0115.1;1.45393,MA0116.1;2.9994,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;1.46638,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.221129,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;1.813,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.483275,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;4.98884,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;1.88496,MA0155.1;0.533581,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.309472,MA0163.1;1.37853,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.0270533,MA0102.2;1.75932,MA0258.1;1.07498,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:28, 22 January 2013


Full id: C2173_CD14_Hepatocyte_liver_Monocytederived_Macrophage_myeloma_lung



Phase1 CAGE Peaks

Hg19::chr11:914812..914866,-p3@CHID1
Hg19::chr6:31895467..31895479,+p4@C2
p6@CFB
Hg19::chr6:31895480..31895530,+p1@C2
Hg19::chr7:150488653..150488682,-p@chr7:150488653..150488682
-


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:0003813classical-complement-pathway C3/C5 convertase activity0.00523960908983869
GO:0006032chitin catabolic process0.0112254201983592
GO:0006046N-acetylglucosamine catabolic process0.0112254201983592
GO:0006043glucosamine catabolic process0.0112254201983592
GO:0006030chitin metabolic process0.0112254201983592
GO:0004568chitinase activity0.0112254201983592
GO:0046348amino sugar catabolic process0.0112254201983592
GO:0044247cellular polysaccharide catabolic process0.0122221556631645
GO:0000272polysaccharide catabolic process0.0122221556631645
GO:0006958complement activation, classical pathway0.0134185936103104
GO:0002455humoral immune response mediated by circulating immunoglobulin0.0134185936103104
GO:0006044N-acetylglucosamine metabolic process0.0134185936103104
GO:0006041glucosamine metabolic process0.0134185936103104
GO:0006956complement activation0.0134185936103104
GO:0002541activation of plasma proteins during acute inflammatory response0.0134185936103104
GO:0006040amino sugar metabolic process0.0134185936103104
GO:0016064immunoglobulin mediated immune response0.0151252863041258
GO:0019724B cell mediated immunity0.0151252863041258
GO:0002253activation of immune response0.0155187118245836
GO:0002449lymphocyte mediated immunity0.0155187118245836
GO:0006959humoral immune response0.0155187118245836
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0155187118245836
GO:0002250adaptive immune response0.0155187118245836
GO:0002443leukocyte mediated immunity0.0155187118245836
GO:0002526acute inflammatory response0.0155187118245836
GO:0044264cellular polysaccharide metabolic process0.0155187118245836
GO:0050778positive regulation of immune response0.0155187118245836
GO:0005976polysaccharide metabolic process0.0155187118245836
GO:0002684positive regulation of immune system process0.0155187118245836
GO:0050776regulation of immune response0.0168773365271673
GO:0002682regulation of immune system process0.0168773365271673
GO:0051240positive regulation of multicellular organismal process0.0171661505175509
GO:0002252immune effector process0.017437343782983
GO:0045087innate immune response0.0175388820935643
GO:0044275cellular carbohydrate catabolic process0.0270582014484685
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0270582014484685
GO:0016052carbohydrate catabolic process0.0270582014484685
GO:0005764lysosome0.0270582014484685
GO:0000323lytic vacuole0.0270582014484685
GO:0016798hydrolase activity, acting on glycosyl bonds0.0287249603360411
GO:0016787hydrolase activity0.0289680995531216
GO:0005773vacuole0.0289680995531216
GO:0051239regulation of multicellular organismal process0.0336157169153266
GO:0006954inflammatory response0.0345049587537292
GO:0004252serine-type endopeptidase activity0.0385836416675041
GO:0008236serine-type peptidase activity0.0417957633034446
GO:0017171serine hydrolase activity0.0417957633034446
GO:0009611response to wounding0.0458872597308855
GO:0043285biopolymer catabolic process0.0482229001898716
GO:0044260cellular macromolecule metabolic process0.0493324365086639



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 organism6.81e-28114
bone marrow2.39e-2376
immune system6.79e-2393
bone element5.11e-2082
hematopoietic system1.77e-1998
blood island1.77e-1998
hemolymphoid system9.90e-19108
skeletal element1.12e-1790
skeletal system4.44e-17100
organ4.56e-14503
germ layer5.07e-09560
germ layer / neural crest5.07e-09560
embryonic tissue5.07e-09560
presumptive structure5.07e-09560
germ layer / neural crest derived structure5.07e-09560
epiblast (generic)5.07e-09560
musculoskeletal system7.09e-09167
embryonic structure7.89e-09564
anatomical system1.21e-08624
anatomical group1.56e-08625
multi-cellular organism3.49e-08656
developing anatomical structure8.20e-08581
embryo1.22e-07592
neural tube1.63e-0756
neural rod1.63e-0756
future spinal cord1.63e-0756
neural keel1.63e-0756


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
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.11.41335
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
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
MA0069.14.32878
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.380957
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
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
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.12.95284
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
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.11.813
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.24.98884
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.88496
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0270533
MA0102.21.75932
MA0258.11.07498
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
BHLHE40#8553222.43590677348870.002891464496853120.0156369956807603
FOXA2#3170212.31523187633260.009361916285467240.0353347972584263
HDAC2#3066310.06171517746970.00156372754474740.00992187977192428
HNF4A#3172211.56614518147680.01057585681762490.0390611419236811
HNF4G#3174214.37671126322340.006924169980439180.0293000035892828
RXRA#6256315.055962854350.0004758307997303580.00433641299241177
STAT1#6772210.35329374859960.01310777476171260.0464858870704779
STAT2#6773232.63188559322030.001379588775125520.00898160279798865
USF1#739134.771124457905970.01370465887188020.0482781012554489



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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