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Coexpression cluster:C3334: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0042953!lipoprotein transport!0.00255108298212802!23390$GO:0019706!protein-cysteine S-palmitoleyltransferase activity!0.00255108298212802!23390$GO:0019707!protein-cysteine S-acyltransferase activity!0.00255108298212802!23390$GO:0016417!S-acyltransferase activity!0.00640284617945621!23390$GO:0015031!protein transport!0.00640284617945621!23033;23390$GO:0016409!palmitoyltransferase activity!0.00640284617945621!23390$GO:0045184!establishment of protein localization!0.00640284617945621!23033;23390$GO:0008104!protein localization!0.00640284617945621!23033;23390$GO:0033036!macromolecule localization!0.00640284617945621!23033;23390$GO:0043123!positive regulation of I-kappaB kinase/NF-kappaB cascade!0.0308358649373065!23390$GO:0030659!cytoplasmic vesicle membrane!0.0308358649373065!23390$GO:0044433!cytoplasmic vesicle part!0.0308358649373065!23390$GO:0043122!regulation of I-kappaB kinase/NF-kappaB cascade!0.0308358649373065!23390$GO:0012506!vesicle membrane!0.0308358649373065!23390$GO:0007249!I-kappaB kinase/NF-kappaB cascade!0.035388549833398!23390$GO:0009967!positive regulation of signal transduction!0.036510769983116!23390$GO:0006810!transport!0.0481393143616867!23033;23390$GO:0008415!acyltransferase activity!0.0481393143616867!23390$GO:0016747!transferase activity, transferring groups other than amino-acyl groups!0.0481393143616867!23390$GO:0051234!establishment of localization!0.0481393143616867!23033;23390
|gostat_on_coexpression_clusters=GO:0042953!lipoprotein transport!0.00255108298212802!23390$GO:0019706!protein-cysteine S-palmitoleyltransferase activity!0.00255108298212802!23390$GO:0019707!protein-cysteine S-acyltransferase activity!0.00255108298212802!23390$GO:0016417!S-acyltransferase activity!0.00640284617945621!23390$GO:0015031!protein transport!0.00640284617945621!23033;23390$GO:0016409!palmitoyltransferase activity!0.00640284617945621!23390$GO:0045184!establishment of protein localization!0.00640284617945621!23033;23390$GO:0008104!protein localization!0.00640284617945621!23033;23390$GO:0033036!macromolecule localization!0.00640284617945621!23033;23390$GO:0043123!positive regulation of I-kappaB kinase/NF-kappaB cascade!0.0308358649373065!23390$GO:0030659!cytoplasmic vesicle membrane!0.0308358649373065!23390$GO:0044433!cytoplasmic vesicle part!0.0308358649373065!23390$GO:0043122!regulation of I-kappaB kinase/NF-kappaB cascade!0.0308358649373065!23390$GO:0012506!vesicle membrane!0.0308358649373065!23390$GO:0007249!I-kappaB kinase/NF-kappaB cascade!0.035388549833398!23390$GO:0009967!positive regulation of signal transduction!0.036510769983116!23390$GO:0006810!transport!0.0481393143616867!23033;23390$GO:0008415!acyltransferase activity!0.0481393143616867!23390$GO:0016747!transferase activity, transferring groups other than amino-acyl groups!0.0481393143616867!23390$GO:0051234!establishment of localization!0.0481393143616867!23033;23390
|id=C3334
|id=C3334
|ontology_enrichment_celltype=CL:0000738!1.93e-12!140;CL:0000037!4.40e-11!172;CL:0000566!4.40e-11!172;CL:0002031!1.49e-10!124;CL:0002032!1.61e-09!165;CL:0000837!1.61e-09!165;CL:0000988!2.55e-09!182;CL:0002087!6.44e-09!119
|ontology_enrichment_celltype=CL:0000738!1.35e-11!136;CL:0000037!2.79e-10!168;CL:0000566!2.79e-10!168;CL:0002031!5.15e-10!120;CL:0002032!5.93e-09!161;CL:0000837!5.93e-09!161;CL:0000988!1.70e-08!177;CL:0002087!1.79e-08!115
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.60e-40!115;UBERON:0001049!2.19e-27!57;UBERON:0005068!2.19e-27!57;UBERON:0006241!2.19e-27!57;UBERON:0007135!2.19e-27!57;UBERON:0001017!1.24e-24!82;UBERON:0003080!4.66e-24!42;UBERON:0002780!5.47e-24!41;UBERON:0001890!5.47e-24!41;UBERON:0006240!5.47e-24!41;UBERON:0002616!5.11e-23!59;UBERON:0005743!1.33e-22!86;UBERON:0000073!1.59e-22!94;UBERON:0001016!1.59e-22!94;UBERON:0000955!3.55e-22!69;UBERON:0006238!3.55e-22!69;UBERON:0002020!1.47e-19!34;UBERON:0003528!1.47e-19!34;UBERON:0001893!1.61e-19!34;UBERON:0002791!5.87e-19!33;UBERON:0001869!1.75e-18!32;UBERON:0002346!7.46e-15!90;UBERON:0002619!9.16e-15!22;UBERON:0000956!2.97e-14!25;UBERON:0000203!2.97e-14!25;UBERON:0003075!4.27e-14!86;UBERON:0007284!4.27e-14!86;UBERON:0001950!1.72e-13!20;UBERON:0003056!1.52e-11!61;UBERON:0000153!2.72e-11!129;UBERON:0007811!2.72e-11!129;UBERON:0000033!4.00e-10!123;UBERON:0000924!1.74e-09!173;UBERON:0006601!1.74e-09!173;UBERON:0004121!7.06e-09!169;UBERON:0002420!7.55e-07!9;UBERON:0007245!7.55e-07!9;UBERON:0010009!7.55e-07!9;UBERON:0010011!7.55e-07!9;UBERON:0000454!7.55e-07!9;UBERON:0002308!8.48e-07!9;UBERON:0000125!8.48e-07!9
|ontology_enrichment_uberon=UBERON:0007023!1.41e-38!114;UBERON:0001049!1.68e-26!56;UBERON:0005068!1.68e-26!56;UBERON:0006241!1.68e-26!56;UBERON:0007135!1.68e-26!56;UBERON:0000073!7.97e-25!53;UBERON:0002616!7.97e-25!53;UBERON:0001017!8.66e-24!81;UBERON:0001016!2.20e-23!89;UBERON:0002780!2.23e-23!41;UBERON:0001890!2.23e-23!41;UBERON:0003080!2.23e-23!41;UBERON:0006240!2.23e-23!41;UBERON:0000955!1.21e-20!68;UBERON:0006238!1.21e-20!68;UBERON:0003528!6.17e-19!34;UBERON:0002020!6.17e-19!34;UBERON:0001893!6.79e-19!34;UBERON:0001869!6.54e-18!32;UBERON:0002791!6.69e-18!32;UBERON:0002346!3.34e-15!86;UBERON:0003075!1.47e-14!82;UBERON:0007284!1.47e-14!82;UBERON:0002619!1.65e-14!22;UBERON:0000956!7.16e-14!25;UBERON:0000203!7.16e-14!25;UBERON:0001950!3.21e-13!20;UBERON:0003056!2.28e-11!61;UBERON:0011216!1.71e-09!223;UBERON:0010371!3.29e-09!104;UBERON:0004121!9.45e-09!171;UBERON:0000924!9.45e-09!171;UBERON:0006601!9.45e-09!171;UBERON:0002420!7.95e-07!9;UBERON:0007245!7.95e-07!9;UBERON:0010009!7.95e-07!9;UBERON:0010011!7.95e-07!9;UBERON:0000454!7.95e-07!9
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321045334710569!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319551693661536!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275839527698832!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328397956657645
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321045334710569!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319551693661536!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275839527698832!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328397956657645
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526,0.0906475,0.0558058,0.0443426,0.166024,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.0117175,0.0330727,0.0694567,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.0470027,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.0458068,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.141463,0.167267,0.140622,0.0889592,4.27652e-05,0.0458479,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.109194,0.128564,0.131452,0.0306206,0.00327218,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.0425274,0.153605,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.188967,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,9.26534e-06,3.18684e-05,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.0266106,0.057168,0.234298,0.0759837,0.286863,0.0122477,0.194941,0.0257725,0.101607,0.00771936,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.0058211,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.0461822,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.220462,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.0362615,0.0590944,0.247324,0.0169521,0.218229,0.231073,0.0020598,0.0170505,0.0360851,0.0021796,0.131093,0.0434602,0.133616,0.0177337,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.0966095,0.381071,0.216033,0.276075,0.432035,0.0411943,0.390366,0.48809,0.50058,0.443185,0.522904,6.58045e-05,0.000283689,0.227104,0.518585,0.0167433,0.38649,0.284625,0.0344717,0.192225,0.0108655,0.28907,0.164197,0.462688,0.287881,0.0556235,0.478174,0.336276,0.468444,0.258219,0.119142,0.243383,0.000933637,0.390974,0.0458848,0.109758,0.161598,0.013901,0.644754,0.150692,0.0239796,0.37357,0.000199981,0.138234,0.069689,0.000558506,0.000852086,0.20342,0.200493,0.20558,0.300504,0.25656,0.107337,0.349197,0.383291,0.156104,0.141318,0.411941,0.00477789,0.314438,0.0720718,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.0674279,0.616388,0.0978616,0.516511,0.322213,0.28903,0.33942,0.243065,0.387276,0.522605,0.00143411,0.0433137,0.222037,0.416621,0.416292,0.462712,0.00246111,0.579431,0.204817,0.452428,0.138871,0.027191,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.0393909,0.408861,0.365487,0.534741,0.0889149,0.0109626,0.236011,0.203486,0.273398,0.0816179,0.4466,0.351067,0.275347,0.0830022,0.305885,0.241132,0.371414,0.30666,0.303709,0.0323359,0.0867777,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.129584,0.601877,0.307334,0.459728,0.283463,0.563586,0.472935,0.0932845,0.273281,0.368095,0.275089,0.384593,0.0283414,0.359231,0.339729,0.197805,0.24107,0.387069,0.332774,0.173874,0.299887,0.0814305,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.0386691,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.0358457,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.0285999,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.0204324,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.0352561,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604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}}
}}

Revision as of 15:01, 19 October 2012


Full id: C3334_cerebellum_pineal_occipital_Dendritic_parietal_medial_pituitary



Phase1 CAGE Peaks

Hg19::chr12:77158021..77158045,+p1@ZDHHC17
Hg19::chr16:2723378..2723446,-p1@ERVK13-1
Hg19::chr6:83777374..83777456,+p1@DOPEY1


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:0042953lipoprotein transport0.00255108298212802
GO:0019706protein-cysteine S-palmitoleyltransferase activity0.00255108298212802
GO:0019707protein-cysteine S-acyltransferase activity0.00255108298212802
GO:0016417S-acyltransferase activity0.00640284617945621
GO:0015031protein transport0.00640284617945621
GO:0016409palmitoyltransferase activity0.00640284617945621
GO:0045184establishment of protein localization0.00640284617945621
GO:0008104protein localization0.00640284617945621
GO:0033036macromolecule localization0.00640284617945621
GO:0043123positive regulation of I-kappaB kinase/NF-kappaB cascade0.0308358649373065
GO:0030659cytoplasmic vesicle membrane0.0308358649373065
GO:0044433cytoplasmic vesicle part0.0308358649373065
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0308358649373065
GO:0012506vesicle membrane0.0308358649373065
GO:0007249I-kappaB kinase/NF-kappaB cascade0.035388549833398
GO:0009967positive regulation of signal transduction0.036510769983116
GO:0006810transport0.0481393143616867
GO:0008415acyltransferase activity0.0481393143616867
GO:0016747transferase activity, transferring groups other than amino-acyl groups0.0481393143616867
GO:0051234establishment of localization0.0481393143616867



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 organism1.41e-38114
neural tube1.68e-2656
neural rod1.68e-2656
future spinal cord1.68e-2656
neural keel1.68e-2656
regional part of nervous system7.97e-2553
regional part of brain7.97e-2553
central nervous system8.66e-2481
nervous system2.20e-2389
regional part of forebrain2.23e-2341
forebrain2.23e-2341
anterior neural tube2.23e-2341
future forebrain2.23e-2341
brain1.21e-2068
future brain1.21e-2068
brain grey matter6.17e-1934
gray matter6.17e-1934
telencephalon6.79e-1934
cerebral hemisphere6.54e-1832
regional part of telencephalon6.69e-1832
neurectoderm3.34e-1586
neural plate1.47e-1482
presumptive neural plate1.47e-1482
regional part of cerebral cortex1.65e-1422
cerebral cortex7.16e-1425
pallium7.16e-1425
neocortex3.21e-1320
pre-chordal neural plate2.28e-1161
organ system subdivision1.71e-09223
ecto-epithelium3.29e-09104
ectoderm-derived structure9.45e-09171
ectoderm9.45e-09171
presumptive ectoderm9.45e-09171
basal ganglion7.95e-079
nuclear complex of neuraxis7.95e-079
aggregate regional part of brain7.95e-079
collection of basal ganglia7.95e-079
cerebral subcortex7.95e-079


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
E2F6#187635.017155731697390.00791769806886330.0321045334710569
EGR1#195834.988179094810140.008056488137383440.0319551693661536
SIN3A#2594235.408884726815140.006318961977991520.0275839527698832
YY1#752834.911170749853860.008441455341808260.0328397956657645



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.