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Difference between revisions of "Coexpression cluster:C4880"

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|full_id=C4880_seminal_lung_ductus_serous_clear_epididymis_kidney
 
|full_id=C4880_seminal_lung_ductus_serous_clear_epididymis_kidney
 
|id=C4880
 
|id=C4880
|ontology_enrichment_celltype=CL:0002541!3.83e-07!3
+
|ontology_enrichment_celltype=CL:0000313!3.06e-09!1
|ontology_enrichment_disease=
+
|ontology_enrichment_disease=DOID:2152!3.06e-09!1
|ontology_enrichment_uberon=UBERON:0007023!1.25e-23!115;UBERON:0006947!5.91e-16!3;UBERON:0004054!5.91e-16!3;UBERON:0005904!4.41e-12!4;UBERON:0000007!6.88e-11!2;UBERON:0003101!6.48e-10!22;UBERON:0000079!6.48e-10!22;UBERON:0005156!2.71e-09!59;UBERON:0000990!2.71e-09!59;UBERON:0003135!2.03e-07!11;UBERON:0000476!3.83e-07!3;UBERON:0000920!3.83e-07!3
+
|ontology_enrichment_uberon=UBERON:0006947!7.86e-24!3;UBERON:0004054!7.86e-24!3;UBERON:0005904!5.01e-18!4;UBERON:0000007!5.83e-16!2;UBERON:0007023!1.25e-13!114;UBERON:0005156!2.47e-13!59;UBERON:0000990!2.47e-13!59;UBERON:0003101!7.86e-12!22;UBERON:0000079!7.86e-12!22;UBERON:0003135!2.88e-11!11;UBERON:0003133!3.29e-11!48;UBERON:0004175!2.38e-10!25;UBERON:0004911!3.06e-09!1;UBERON:0000998!3.31e-09!1;UBERON:0006868!3.31e-09!1;UBERON:0002171!4.19e-09!1;UBERON:0006518!4.19e-09!1;UBERON:0008949!4.19e-09!1;UBERON:0000101!4.19e-09!1;UBERON:0002167!4.19e-09!1;UBERON:0001000!4.52e-09!1;UBERON:0005352!4.52e-09!1;UBERON:0001301!4.89e-09!1;UBERON:0006834!6.16e-09!1;UBERON:0005418!8.36e-09!1;UBERON:0001389!8.36e-09!1;UBERON:0000026!8.36e-09!1;UBERON:0008784!8.36e-09!1;UBERON:0006058!8.36e-09!1;UBERON:0003663!8.36e-09!1;UBERON:0004256!8.36e-09!1;UBERON:0004708!8.36e-09!1;UBERON:0002101!8.36e-09!1;UBERON:0004709!8.36e-09!1;UBERON:0002529!8.36e-09!1;UBERON:0010538!8.36e-09!1;UBERON:0003661!8.36e-09!1;UBERON:0010890!8.36e-09!1;UBERON:0002471!8.36e-09!1;UBERON:0001383!8.36e-09!1;UBERON:0004357!8.36e-09!1;UBERON:0004347!8.36e-09!1;UBERON:0005420!8.36e-09!1;UBERON:0005732!8.36e-09!1;UBERON:0010758!8.36e-09!1;UBERON:0010707!8.36e-09!1;UBERON:0000978!8.36e-09!1;UBERON:0002103!8.36e-09!1;UBERON:0001665!8.36e-09!1;UBERON:0003823!8.36e-09!1;UBERON:0000154!8.36e-09!1;UBERON:0010709!8.36e-09!1;UBERON:0005733!8.36e-09!1;UBERON:0005730!8.36e-09!1;UBERON:0003296!1.99e-08!4;UBERON:0010133!1.99e-08!4;UBERON:0006554!5.46e-07!47;UBERON:0001008!7.94e-07!48;UBERON:0005153!8.46e-07!37
 
|tf_chipseq_enrich=NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310743188452261
 
|tf_chipseq_enrich=NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310743188452261
 
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.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.911304,0.936279,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.216033,0.643768,0.432035,0.722159,0.390366,0.48809,0.50058,0.443185,0.522904,0.875915,0.871256,0.227104,0.00667974,0.617852,0.38649,0.284625,0.504757,0.55194,0.729153,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.777351,0.390974,0.73485,0.683217,0.161598,0.751174,0.644754,0.496032,0.799185,0.37357,0.78509,0.477353,0.78384,0.746954,0.771991,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.0696455,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.0289012,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.78,0.616388,0.408413,0.516511,0.322213,0.656109,0.33942,0.243065,0.387276,0.522605,0.802166,0.537348,0.222037,0.416621,0.416292,0.462712,0.734551,0.579431,0.204817,0.452428,0.138871,0.673493,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.170369,0.408861,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.637444,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.010576,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
 
}}
 
}}

Revision as of 07:19, 19 October 2012


Full id: C4880_seminal_lung_ductus_serous_clear_epididymis_kidney



Phase1 CAGE Peaks

  Short description
Hg19::chrX:93855166..93855179,- p@chrX:93855166..93855179
-
Hg19::chrX:93855198..93855209,- p@chrX:93855198..93855209
-
Hg19::chrX:93855260..93855292,- p@chrX:93855260..93855292
-


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
serous secreting cell3.06e-091
Uber Anatomy
Ontology termp-valuen
male genital duct7.86e-243
internal male genitalia7.86e-243
duct of male reproductive system5.01e-184
pituitary gland5.83e-162
adult organism1.25e-13114
reproductive structure2.47e-1359
reproductive system2.47e-1359
male organism7.86e-1222
male reproductive system7.86e-1222
male reproductive organ2.88e-1111
reproductive organ3.29e-1148
internal genitalia2.38e-1025
epithelium of female gonad3.06e-091
seminal vesicle3.31e-091
seminal fluid secreting gland3.31e-091
lower lobe of right lung4.19e-091
right lung lobe4.19e-091
lower lobe of lung4.19e-091
lobe of lung4.19e-091
right lung4.19e-091
vas deferens4.52e-091
spermatic cord4.52e-091
epididymis4.89e-091
uterus or analog6.16e-091
hindlimb bud8.36e-091
soleus muscle8.36e-091
appendage8.36e-091
lower limb segment8.36e-091
multi-limb segment region8.36e-091
hindlimb muscle8.36e-091
hindlimb zeugopod muscle8.36e-091
paired limb/fin8.36e-091
limb8.36e-091
pelvic appendage8.36e-091
limb segment8.36e-091
paired limb/fin segment8.36e-091
limb muscle8.36e-091
pelvic complex muscle8.36e-091
zeugopod8.36e-091
muscle of leg8.36e-091
paired limb/fin bud8.36e-091
limb bud8.36e-091
pelvic appendage bud8.36e-091
limb/fin field8.36e-091
subdivision of organism along appendicular axis8.36e-091
appendage girdle complex8.36e-091
leg8.36e-091
hindlimb8.36e-091
triceps surae8.36e-091
hindlimb zeugopod8.36e-091
posterior region of body8.36e-091
pelvic complex8.36e-091
limb field8.36e-091
hindlimb/pelvic fin field8.36e-091
gland of diencephalon1.99e-084
neuroendocrine gland1.99e-084
urinary system structure5.46e-0747
renal system7.94e-0748
epithelial bud8.46e-0737
Disease
Ontology termp-valuen
ovary epithelial cancer3.06e-091


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
NR3C1#2908314.9730233311730.0002978331194675480.00310743188452261



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.