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Coexpression cluster:C3207: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.39e-49!115;UBERON:0001049!1.31e-25!57;UBERON:0005068!1.31e-25!57;UBERON:0006241!1.31e-25!57;UBERON:0007135!1.31e-25!57;UBERON:0001017!3.14e-24!82;UBERON:0002616!4.41e-23!59;UBERON:0000955!3.55e-22!69;UBERON:0006238!3.55e-22!69;UBERON:0005743!5.79e-22!86;UBERON:0000073!3.44e-21!94;UBERON:0001016!3.44e-21!94;UBERON:0002346!9.52e-20!90;UBERON:0003080!1.89e-19!42;UBERON:0002780!6.93e-19!41;UBERON:0001890!6.93e-19!41;UBERON:0006240!6.93e-19!41;UBERON:0003075!7.69e-19!86;UBERON:0007284!7.69e-19!86;UBERON:0002020!2.15e-15!34;UBERON:0003528!2.15e-15!34;UBERON:0001893!3.12e-15!34;UBERON:0002791!8.62e-15!33;UBERON:0001869!3.06e-14!32;UBERON:0000153!3.32e-14!129;UBERON:0007811!3.32e-14!129;UBERON:0000033!4.18e-13!123;UBERON:0000924!3.33e-12!173;UBERON:0006601!3.33e-12!173;UBERON:0003056!4.87e-12!61;UBERON:0002619!8.29e-12!22;UBERON:0004121!1.87e-11!169;UBERON:0000956!4.46e-11!25;UBERON:0000203!4.46e-11!25;UBERON:0000477!6.89e-11!286;UBERON:0001950!9.03e-11!20;UBERON:0004111!4.39e-10!241;UBERON:0000025!1.19e-09!194;UBERON:0003076!2.41e-07!15;UBERON:0003057!2.41e-07!15;UBERON:0000475!5.36e-07!365
|ontology_enrichment_uberon=UBERON:0007023!7.45e-48!114;UBERON:0001017!2.75e-25!81;UBERON:0001049!3.88e-25!56;UBERON:0005068!3.88e-25!56;UBERON:0006241!3.88e-25!56;UBERON:0007135!3.88e-25!56;UBERON:0000073!2.58e-23!53;UBERON:0002616!2.58e-23!53;UBERON:0001016!3.01e-23!89;UBERON:0000955!2.05e-22!68;UBERON:0006238!2.05e-22!68;UBERON:0002346!1.08e-19!86;UBERON:0011216!2.27e-19!223;UBERON:0003075!1.04e-18!82;UBERON:0007284!1.04e-18!82;UBERON:0002780!1.99e-18!41;UBERON:0001890!1.99e-18!41;UBERON:0003080!1.99e-18!41;UBERON:0006240!1.99e-18!41;UBERON:0003528!1.24e-15!34;UBERON:0002020!1.24e-15!34;UBERON:0001893!2.08e-15!34;UBERON:0002791!2.00e-14!32;UBERON:0001869!2.65e-14!32;UBERON:0010314!1.59e-13!132;UBERON:0002619!1.85e-12!22;UBERON:0004121!4.15e-12!171;UBERON:0000924!4.15e-12!171;UBERON:0006601!4.15e-12!171;UBERON:0001950!1.35e-11!20;UBERON:0000477!1.62e-11!373;UBERON:0003056!2.17e-11!61;UBERON:0000956!2.33e-11!25;UBERON:0000203!2.33e-11!25;UBERON:0010371!4.04e-11!104;UBERON:0003076!6.64e-08!15;UBERON:0003057!6.64e-08!15;UBERON:0004111!9.24e-08!240;UBERON:0000025!5.50e-07!192
|tf_chipseq_enrich=ZZZ3#26009;1:79.8044041450777:0.012478437908258:0.0451524642864759
|tf_chipseq_enrich=ZZZ3#26009;1:79.8044041450777:0.012478437908258:0.0451524642864759
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762,0.0828956,0.0666953,0.0177068,0.00643465,0.219383,0.000810221,0.19559,0.00915124,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.015204,0.0876426,0.0952322,0.0112557,0.222432,0.107043,2.20551e-05,0.00481323,0.173708,0.141119,0.0241568,0.0300692,0.131551,0.0445237,0.052362,0.00179985,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.0443426,0.166024,0.000481141,0.0145999,0.0656973,0.211746,0.220538,0.00330134,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,1.61852e-06,0.0015938,2.02233e-05,0.174921,0.370421,0.0330727,0.348757,0.02609,0.0394698,0.0596469,0.00236266,0.122476,0.108872,0.00628729,0.26144,0.0286025,0.00896808,0.144567,0.038848,0.0874516,0.0550279,0.000558597,0.253693,0.0254773,0.190048,0.131088,0.090504,0.237101,0.286988,0.0761239,4.60407e-05,0.0818785,0.0178107,0.335058,0.147698,0.141463,0.0148418,0.140622,0.0889592,0.309588,0.0458479,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.00864322,0.131452,0.323837,0.120459,0.051838,0.00511251,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.000585365,0.0741807,0.0425274,0.0122266,1.6691e-09,0.21727,0.289306,0.119215,0.0198413,0.0168693,0.0465298,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.300597,0.0713214,0.00014048,0.291114,0.0355833,0.00824114,0.175094,0.00352878,0.0225581,0.206454,0.00206897,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.00631005,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.0298844,0.0759837,0.286863,8.96704e-07,0.194941,0.218271,1.07646e-07,2.14872e-07,0.172982,0.0661495,0.151597,0.0626744,0.0195983,0.148574,0.504592,0.155821,6.54495e-05,0.0919008,0.0602373,0.0109522,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.00326415,0.0461822,0.11903,0.0838874,0.331451,0.113145,0.112651,0.00125943,0.00102368,0.0948451,0.0384217,0.0339656,0.140533,0.00515192,0.257598,0.103667,0.113069,0.025556,0.0149597,0.09066,0.000306535,0.166967,0.188651,0.0813902,0.184948,3.03264e-05,0.311847,0.511859,0.0590944,0.0334734,0.178389,0.218229,0.0290303,0.0972686,0.0743925,0.0360851,0.0021796,0.00899487,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.00858901,0.0210947,0.00131691,0.00255501,0.00327292,0.197484,0.0919774,0.0750251,0.406019,0.0841307,0.580441,0.643768,0.11074,0.00207232,0.0140037,0.48809,0.0334527,0.0217093,0.00100396,0.3468,0.151996,0.227104,0.518585,0.000486104,0.38649,1.4731e-06,0.156746,2.12137e-05,0.0108655,0.0465139,0.164197,0.462688,0.287881,0.574635,0.00445792,0.0642229,0.468444,0.258219,3.00528e-06,5.14971e-07,0.000933637,0.0140783,0.0458848,3.45229e-06,0.161598,0.00310283,0.277094,0.0323708,0.00136122,0.0805771,0.000199981,0.138234,0.199161,0.00292516,0.00415823,0.20342,0.200493,0.20558,0.0505073,0.25656,0.107337,0.349197,0.383291,0.156104,0.0104921,0.00217346,0.0961477,0.314438,0.0101316,0.163828,0.230581,0.120226,0.28424,0.562405,0.0556238,0.0175523,0.0442318,0.194707,0.24884,0.408413,0.0374737,0.0073454,0.656109,0.000885969,0.0700181,0.387276,0.169614,0.481611,0.0433137,0.222037,1.63765e-06,2.13631e-05,0.462712,0.0115406,0.579431,0.204817,0.000401229,0.138871,0.103502,0.166905,0.19783,0.0833851,0.000645205,0.0289164,0.0163316,0.00818864,0.0805711,0.170369,0.0980968,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.019895,0.0524515,0.241132,0.0118241,0.30666,0.303709,0.495883,0.386538,0.035296,0.250964,0.383276,0.00360665,0.504711,0.00213139,0.0355483,0.196976,0.191517,0.463751,0.0145214,0.0529819,0.127092,6.78075e-08,0.563586,0.135386,0.0151656,0.0413011,0.0780405,2.19858e-05,0.00157463,0.00444763,0.0740334,0.339729,0.197805,0.608187,0.387069,6.46213e-05,0.52832,0.000506965,0.266492,0.205413,0.0165618,0.0779009,0.276869,0.022685,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.0139948,0.19104,0.163057,0.0260582,0.000102347,0.0900729,0.000155666,0.0146333,0.00329437,0.0828367,1.4588e-05,0.000101329,0.447185,0.179412,0.193601,0.220904,0.0269454,0.341681,0.0542164,0.21801,0.198614,0.186804,0.123324,0.00155473,0.0325925,0.0933115,0.12405,0.0172483,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.0285999,0.162145,0.00241368,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.00753169,4.46698e-06,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.0377094,0.0223377,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.0273485,0.000211932,0.173026,0.0215816,0.0102599,0.197112,0.240478,0.156465,0.13108,0.256963,0.0269005,0.172134,0.176789,0.0969345,0.202137,0.310405,0.00467879,0.000125641,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.0240944,0.187731,0.233626,0.189559,0.0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}}
}}

Revision as of 14:53, 19 October 2012


Full id: C3207_cerebellum_thyroid_Mesenchymal_ductus_seminal_vagina_throat



Phase1 CAGE Peaks

Hg19::chr11:85338366..85338393,-p9@DLG2
Hg19::chr19:3029177..3029261,-p1@TLE2
Hg19::chr3:114819124..114819200,-p3@ZBTB20


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><br>


Uber Anatomy
Ontology termp-valuen
adult organism7.45e-48114
central nervous system2.75e-2581
neural tube3.88e-2556
neural rod3.88e-2556
future spinal cord3.88e-2556
neural keel3.88e-2556
regional part of nervous system2.58e-2353
regional part of brain2.58e-2353
nervous system3.01e-2389
brain2.05e-2268
future brain2.05e-2268
neurectoderm1.08e-1986
organ system subdivision2.27e-19223
neural plate1.04e-1882
presumptive neural plate1.04e-1882
regional part of forebrain1.99e-1841
forebrain1.99e-1841
anterior neural tube1.99e-1841
future forebrain1.99e-1841
brain grey matter1.24e-1534
gray matter1.24e-1534
telencephalon2.08e-1534
regional part of telencephalon2.00e-1432
cerebral hemisphere2.65e-1432
structure with developmental contribution from neural crest1.59e-13132
regional part of cerebral cortex1.85e-1222
ectoderm-derived structure4.15e-12171
ectoderm4.15e-12171
presumptive ectoderm4.15e-12171
neocortex1.35e-1120
anatomical cluster1.62e-11373
pre-chordal neural plate2.17e-1161
cerebral cortex2.33e-1125
pallium2.33e-1125
ecto-epithelium4.04e-11104
posterior neural tube6.64e-0815
chordal neural plate6.64e-0815
anatomical conduit9.24e-08240
tube5.50e-07192


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


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

TF#promotersEnrichmentp-valueq-value
ZZZ3#26009179.80440414507770.0124784379082580.0451524642864759



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.