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Coexpression cluster:C3241: Difference between revisions

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|full_id=C3241_thyroid_ductus_seminal_throat_epididymis_serous_renal
|full_id=C3241_thyroid_ductus_seminal_throat_epididymis_serous_renal
|id=C3241
|id=C3241
|ontology_enrichment_celltype=CL:0000945!9.80e-27!24;CL:0000826!9.80e-27!24;CL:0000236!1.91e-16!14;CL:0000542!9.23e-11!53;CL:0000051!9.23e-11!53;CL:0000838!7.36e-10!52;CL:0002322!5.23e-08!5
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:12603!1.69e-09!1
|ontology_enrichment_uberon=UBERON:0007023!2.82e-08!115;UBERON:0003135!7.02e-07!11;UBERON:0006947!7.07e-07!3;UBERON:0004054!7.07e-07!3
|ontology_enrichment_uberon=UBERON:0006947!8.83e-26!3;UBERON:0004054!8.83e-26!3;UBERON:0005904!1.71e-19!4;UBERON:0000341!2.44e-17!2;UBERON:0004175!4.37e-15!25;UBERON:0003135!3.13e-12!11;UBERON:0000998!7.98e-10!1;UBERON:0006868!7.98e-10!1;UBERON:0001000!8.68e-10!1;UBERON:0005352!8.68e-10!1;UBERON:0005156!9.88e-10!59;UBERON:0000990!9.88e-10!59;UBERON:0003133!1.11e-09!48;UBERON:0001301!1.12e-09!1;UBERON:0003101!3.24e-09!22;UBERON:0000079!3.24e-09!22;UBERON:0002372!3.83e-09!1;UBERON:0001961!3.83e-09!1;UBERON:0001744!3.83e-09!1;UBERON:0001735!3.83e-09!1;UBERON:0006834!4.50e-09!1;UBERON:0005795!7.69e-09!22;UBERON:0007023!5.13e-08!114;UBERON:0000974!8.74e-08!10;UBERON:0002046!1.36e-07!5;UBERON:0004117!1.36e-07!5;UBERON:0007689!1.36e-07!5;UBERON:0007123!1.36e-07!5;UBERON:0003091!1.36e-07!5;UBERON:0009722!3.36e-07!11;UBERON:0007690!3.36e-07!11
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52362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.166024,0.009894,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.013859,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.0791124,0.0330727,0.348757,0.02609,0.0394698,0.0596469,0.103658,0.000337112,0.108872,0.11002,0.26144,0.0286025,0.190156,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.0353101,0.217069,0.190048,0.131088,0.090504,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.0148418,0.000517983,0.0889592,0.0538132,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.00904548,0.00681584,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.153605,0.0232393,0.21727,0.289306,0.119215,0.192475,0.177967,0.188967,0.057571,0.047591,0.392974,0.0608699,0.0163547,0.300597,0.0713214,0.0271723,0.291114,0.0355833,0.125606,0.175094,0.226002,0.76084,0.206454,0.0257531,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.00631005,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.00571044,0.221645,0.057168,0.234298,0.0759837,0.0457643,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.0109522,0.15063,0.0973823,0.0126914,0.0154015,0.193653,0.137219,0.228144,0.0346616,0.0461822,0.11903,0.0838874,0.0622625,0.113145,0.112651,0.186638,0.174776,0.0948451,0.0384217,0.0339656,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0597157,0.0147868,0.0190329,0.0813902,0.0182671,0.156261,0.0546539,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.252227,0.0360851,0.0168763,0.131093,0.0434602,0.133616,0.418146,0.36927,0.0227305,0.407369,0.231447,0.0455669,0.0210947,0.0789454,0.0189483,0.120472,0.197484,0.0919774,0.36145,0.0966095,0.0841307,0.216033,0.643768,0.432035,0.138468,0.390366,0.48809,0.0334527,0.443185,0.169835,0.616975,0.60734,0.227104,0.166658,0.0734371,0.0867545,0.284625,0.0344717,0.192225,0.0437169,0.28907,0.164197,0.0252589,0.287881,0.0556235,0.00445792,0.0642229,0.468444,0.258219,0.119142,0.243383,0.442897,0.0889613,0.0458848,0.109758,0.161598,0.405056,0.277094,0.150692,0.476802,0.37357,0.454657,0.477353,0.78384,0.160298,0.185744,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.0556238,0.181415,0.282286,0.446891,0.24884,0.408413,0.516511,0.322213,0.28903,0.00873429,0.00285083,0.0871388,0.522605,0.802166,0.0433137,0.222037,0.102227,0.416292,0.462712,0.0457685,0.579431,0.204817,0.122646,0.138871,0.308032,0.166905,0.19783,0.0833851,0.056391,0.0289164,0.175199,0.332919,0.0805711,0.0393909,0.0980968,0.365487,0.534741,0.0889149,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.637444,0.305885,0.241132,0.371414,0.30666,0.303709,0.15059,0.0867777,0.508064,0.250964,0.383276,0.457886,0.00582796,0.220231,0.159791,0.196976,0.191517,0.0254647,0.00258603,0.307334,0.127092,0.283463,0.563586,0.135386,0.399569,0.273281,0.0780405,0.275089,0.0858306,0.47795,0.359231,0.0656472,0.197805,0.608187,0.387069,0.0627969,0.52832,0.299887,0.266492,0.205413,0.17639,0.0779009,0.276869,0.022685,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.0828367,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.00221755,0.341681,0.310674,0.00206345,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.0267847,0.0673329,0.20847,0.266544,0.113092,0.0111711,0.229428,0.0139199,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.00972162,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.0262794,0.195218,0.124213,0.259632,0.0532009,0.180606,0.159884,0.257294,0.150733,0.0254879,0.123917,0.184317,0.185335,0.0723291,0.258496,0.0377094,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.0541163,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.018841,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.0687209,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.0385243,0.131761,0.160658,0.0229018,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.0342254,0.0143647,0.224257,0.0935776,0.327622,0.0276507,0.0232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}}
}}

Revision as of 14:55, 19 October 2012


Full id: C3241_thyroid_ductus_seminal_throat_epididymis_serous_renal



Phase1 CAGE Peaks

Hg19::chr12:115123687..115123734,-p@chr12:115123687..115123734
-
Hg19::chr12:52511996..52512012,-p@chr12:52511996..52512012
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Hg19::chr18:30349623..30349635,+p1@ENST00000426194


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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
male genital duct8.83e-263
internal male genitalia8.83e-263
duct of male reproductive system1.71e-194
throat2.44e-172
internal genitalia4.37e-1525
male reproductive organ3.13e-1211
seminal vesicle7.98e-101
seminal fluid secreting gland7.98e-101
vas deferens8.68e-101
spermatic cord8.68e-101
reproductive structure9.88e-1059
reproductive system9.88e-1059
reproductive organ1.11e-0948
epididymis1.12e-091
male organism3.24e-0922
male reproductive system3.24e-0922
tonsil3.83e-091
mucosa-associated lymphoid tissue3.83e-091
lymphoid tissue3.83e-091
tonsillar ring3.83e-091
uterus or analog4.50e-091
embryonic uterus7.69e-0922
adult organism5.13e-08114
neck8.74e-0810
thyroid gland1.36e-075
pharyngeal pouch1.36e-075
thyroid diverticulum1.36e-075
pharyngeal pouch 21.36e-075
thyroid primordium1.36e-075
entire pharyngeal arch endoderm3.36e-0711
early pharyngeal endoderm3.36e-0711
Disease
Ontology termp-valuen
acute leukemia1.69e-091


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)

{{{tfbs_overrepresentation_jaspar}}}



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


No analysis results for this cluster

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.