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Coexpression cluster:C3207: Difference between revisions

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|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!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
|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 13:58, 5 September 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 organism1.39e-49115
neural tube1.31e-2557
neural rod1.31e-2557
future spinal cord1.31e-2557
neural keel1.31e-2557
central nervous system3.14e-2482
regional part of brain4.41e-2359
brain3.55e-2269
future brain3.55e-2269
regional part of nervous system3.44e-2194
nervous system3.44e-2194
neurectoderm9.52e-2090
anterior neural tube1.89e-1942
regional part of forebrain6.93e-1941
forebrain6.93e-1941
future forebrain6.93e-1941
neural plate7.69e-1986
presumptive neural plate7.69e-1986
gray matter2.15e-1534
brain grey matter2.15e-1534
telencephalon3.12e-1534
regional part of telencephalon8.62e-1533
cerebral hemisphere3.06e-1432
anterior region of body3.32e-14129
craniocervical region3.32e-14129
head4.18e-13123
ectoderm3.33e-12173
presumptive ectoderm3.33e-12173
pre-chordal neural plate4.87e-1261
regional part of cerebral cortex8.29e-1222
ectoderm-derived structure1.87e-11169
cerebral cortex4.46e-1125
pallium4.46e-1125
anatomical cluster6.89e-11286
neocortex9.03e-1120
anatomical conduit4.39e-10241
tube1.19e-09194
posterior neural tube2.41e-0715
chordal neural plate2.41e-0715
organism subdivision5.36e-07365


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.

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