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Coexpression cluster:C4068: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.45e-32!115;UBERON:0001017!8.28e-30!82;UBERON:0001049!1.33e-29!57;UBERON:0005068!1.33e-29!57;UBERON:0006241!1.33e-29!57;UBERON:0007135!1.33e-29!57;UBERON:0005743!2.53e-29!86;UBERON:0002616!2.39e-28!59;UBERON:0000955!6.46e-28!69;UBERON:0006238!6.46e-28!69;UBERON:0000073!6.97e-26!94;UBERON:0001016!6.97e-26!94;UBERON:0003075!8.44e-24!86;UBERON:0007284!8.44e-24!86;UBERON:0000153!1.54e-23!129;UBERON:0007811!1.54e-23!129;UBERON:0002780!4.14e-23!41;UBERON:0001890!4.14e-23!41;UBERON:0006240!4.14e-23!41;UBERON:0003080!6.07e-23!42;UBERON:0002346!7.32e-23!90;UBERON:0000033!3.34e-22!123;UBERON:0001893!2.10e-18!34;UBERON:0002020!2.35e-18!34;UBERON:0003528!2.35e-18!34;UBERON:0002791!7.65e-18!33;UBERON:0003056!1.90e-17!61;UBERON:0001869!4.28e-17!32;UBERON:0004121!9.64e-16!169;UBERON:0000924!1.88e-15!173;UBERON:0006601!1.88e-15!173;UBERON:0000956!6.38e-13!25;UBERON:0000203!6.38e-13!25;UBERON:0002619!2.66e-11!22;UBERON:0000477!8.14e-11!286;UBERON:0000475!1.70e-10!365;UBERON:0001950!4.91e-10!20;UBERON:0000481!1.98e-09!347;UBERON:0000062!2.83e-08!511;UBERON:0003076!8.24e-08!15;UBERON:0003057!8.24e-08!15;UBERON:0000479!3.09e-07!787;UBERON:0002308!5.35e-07!9;UBERON:0000125!5.35e-07!9;UBERON:0004111!6.08e-07!241;UBERON:0002420!7.96e-07!9;UBERON:0007245!7.96e-07!9;UBERON:0010009!7.96e-07!9;UBERON:0010011!7.96e-07!9;UBERON:0000454!7.96e-07!9
|ontology_enrichment_uberon=UBERON:0007023!4.88e-29!114;UBERON:0001049!2.73e-28!56;UBERON:0005068!2.73e-28!56;UBERON:0006241!2.73e-28!56;UBERON:0007135!2.73e-28!56;UBERON:0001017!1.47e-27!81;UBERON:0000073!2.12e-26!53;UBERON:0002616!2.12e-26!53;UBERON:0000955!2.17e-26!68;UBERON:0006238!2.17e-26!68;UBERON:0001016!4.43e-24!89;UBERON:0003075!2.63e-23!82;UBERON:0007284!2.63e-23!82;UBERON:0002780!3.80e-23!41;UBERON:0001890!3.80e-23!41;UBERON:0003080!3.80e-23!41;UBERON:0006240!3.80e-23!41;UBERON:0002346!2.80e-22!86;UBERON:0010314!2.13e-20!132;UBERON:0001893!2.43e-18!34;UBERON:0003528!3.40e-18!34;UBERON:0002020!3.40e-18!34;UBERON:0003056!1.52e-17!61;UBERON:0002791!4.04e-17!32;UBERON:0001869!4.81e-17!32;UBERON:0011216!2.03e-15!223;UBERON:0010371!8.26e-15!104;UBERON:0004121!4.49e-14!171;UBERON:0000924!4.49e-14!171;UBERON:0006601!4.49e-14!171;UBERON:0000956!7.73e-13!25;UBERON:0000203!7.73e-13!25;UBERON:0000481!2.24e-11!342;UBERON:0002619!3.46e-11!22;UBERON:0000477!5.42e-11!373;UBERON:0001950!6.32e-10!20;UBERON:0000062!5.90e-07!503;UBERON:0000125!6.45e-07!9;UBERON:0002308!6.45e-07!9;UBERON:0002420!6.54e-07!9;UBERON:0007245!6.54e-07!9;UBERON:0010009!6.54e-07!9;UBERON:0010011!6.54e-07!9;UBERON:0000454!6.54e-07!9
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279940208838962!EBF1#1879;3:8.906466846569:0.0014152328356098:0.0091622552763608!ESR1#2099;2:20.5124021974363:0.00309974157709518:0.0163139442940054!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00665155960146473!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00485331594122243!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00309586703431156!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248604035708688!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616705523700366!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197309224667367
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0481795,0.199971,0.406014,0.127758,0.175785,2.48127e-06,0.169234,0.0876426,0.0046858,0.0112557,0.00220026,0.107043,0.0043762,0.00481323,0.173708,0.141119,2.04645e-07,0.0300692,0.131551,0.00100623,0.052362,0.0235128,0.153187,0.00327141,0.0974211,1.1672e-06,0.00796449,0.0906475,0.0558058,0.28262,0.517717,0.000481141,0.0145999,0.0656973,0.00188014,0.0021409,0.0801488,0.00294748,0.013859,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.0791124,0.0330727,0.348757,0.02609,0.0394698,0.0596469,0.0178982,0.122476,0.108872,1.62698e-07,0.00370214,0.0286025,0.190156,0.144567,0.038848,0.0874516,0.0015426,0.144067,0.253693,0.00203513,0.190048,1.45197e-05,0.0144628,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.0178107,0.335058,0.147698,0.000527702,0.167267,0.140622,0.0889592,0.0538132,0.00502301,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.00904548,0.00681584,0.0226843,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.00452901,0.0109165,0.0340203,0.0741807,1.22829e-06,0.739716,0.655293,0.21727,0.00514993,0.000310064,0.192475,0.177967,0.547859,0.057571,0.047591,0.0899568,3.93849e-05,0.175319,0.0505407,0.0713214,0.0271723,0.291114,0.0355833,0.000364559,0.0163112,0.0121461,0.519327,0.206454,0.00206897,0.108277,0.0673484,0.108748,0.0494066,0.000158113,0.205732,0.00293103,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.00921075,0.00102818,0.0539144,0.00678942,0.0929549,0.172425,0.104948,0.00217546,0.057168,0.0298844,0.0759837,0.286863,0.152372,0.194941,0.0257725,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.0119616,0.0973823,0.15503,0.000943322,7.53325e-05,0.137219,0.228144,0.00326415,0.0050797,0.11903,0.0838874,0.331451,0.113145,0.00659775,0.186638,0.174776,0.0948451,3.86923e-08,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.0149597,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.161789,0.0590944,0.247324,0.178389,0.218229,0.231073,0.0972686,0.0170505,0.0360851,0.412187,0.00899487,0.0434602,0.133616,0.103051,0.36927,0.449036,0.0162067,0.231447,0.000168888,3.19513e-05,0.0116789,0.0189483,0.022688,0.197484,0.0148336,2.7308e-08,0.0160226,1.12468e-05,0.580441,0.643768,0.0198622,0.00207232,0.000164197,5.54033e-07,0.0334527,0.443185,0.169835,0.875915,0.336835,0.227104,0.518585,0.0734371,0.38649,7.00546e-08,0.156746,0.192225,0.375373,0.0465139,0.164197,0.462688,0.287881,0.574635,0.478174,0.0642229,0.0263888,0.258219,0.446557,0.243383,0.191695,0.390974,0.0458848,0.00120937,0.161598,0.00310283,0.000709044,0.150692,0.00613559,9.75452e-06,0.200632,0.0282154,0.069689,0.0508568,0.0175763,0.20342,0.200493,0.20558,0.300504,0.0361545,0.0189087,0.00960524,0.383291,0.000717871,0.141318,0.411941,0.0961477,0.314438,0.0101316,0.163828,0.230581,0.120226,1.45963e-06,0.562405,0.314429,0.181415,0.00475227,0.00465874,7.94759e-07,0.01635,0.165147,0.0586066,0.656109,0.33942,0.61031,0.387276,0.0391112,0.802166,0.537348,0.222037,2.14873e-05,0.416292,0.462712,0.382478,0.057399,0.204817,0.452428,0.138871,0.000165333,0.000885521,8.25294e-05,0.0833851,0.000645205,0.000585352,0.175199,0.00818864,0.00137548,0.523625,1.87226e-05,0.365487,0.00780726,0.0140668,0.363192,0.236011,0.203486,0.00428131,0.00141394,0.4466,0.351067,0.000346951,0.637444,0.305885,0.241132,0.371414,2.45102e-06,0.303709,0.495883,0.386538,0.508064,0.0345164,0.00154968,0.0243456,0.504711,0.220231,0.509064,0.00149391,0.191517,0.0254647,0.601877,1.29649e-07,0.127092,0.0048173,0.563586,5.55277e-05,0.0932845,0.273281,0.000116083,0.275089,0.384593,0.0283414,0.0740334,0.339729,0.197805,0.608187,0.387069,0.0627969,0.0406989,0.299887,0.634365,0.205413,0.00105378,0.0779009,0.276869,0.205298,0.0337138,0.18966,1.23275e-09,0.00129444,0.0719199,9.06634e-07,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.000373385,0.179412,0.00141426,0.00215229,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.0023439,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.000263373,0.145701,0.00242972,0.00080862,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.00200124,0.0132793,0.00213411,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.00203642,0.123917,0.184317,8.64477e-08,0.0723291,0.00356871,0.261744,0.00166408,0.21382,0.0232077,0.141867,0.00140109,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.0102599,0.197112,0.240478,0.156465,0.13108,0.256963,6.87632e-06,0.172134,0.176789,0.0969345,0.00162178,0.310405,0.280943,0.218161,0.0822373,0.00161996,0.000220289,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.0056723,0.0022498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}}
}}

Revision as of 15:39, 19 October 2012


Full id: C4068_myeloma_Astrocyte_pineal_hippocampus_caudate_cervix_thalamus



Phase1 CAGE Peaks

Hg19::chr21:17566852..17566866,+p5@LINC00478
Hg19::chr21:17566867..17566899,+p2@LINC00478
Hg19::chr21:17566902..17566923,+p8@LINC00478


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 organism4.88e-29114
neural tube2.73e-2856
neural rod2.73e-2856
future spinal cord2.73e-2856
neural keel2.73e-2856
central nervous system1.47e-2781
regional part of nervous system2.12e-2653
regional part of brain2.12e-2653
brain2.17e-2668
future brain2.17e-2668
nervous system4.43e-2489
neural plate2.63e-2382
presumptive neural plate2.63e-2382
regional part of forebrain3.80e-2341
forebrain3.80e-2341
anterior neural tube3.80e-2341
future forebrain3.80e-2341
neurectoderm2.80e-2286
structure with developmental contribution from neural crest2.13e-20132
telencephalon2.43e-1834
brain grey matter3.40e-1834
gray matter3.40e-1834
pre-chordal neural plate1.52e-1761
regional part of telencephalon4.04e-1732
cerebral hemisphere4.81e-1732
organ system subdivision2.03e-15223
ecto-epithelium8.26e-15104
ectoderm-derived structure4.49e-14171
ectoderm4.49e-14171
presumptive ectoderm4.49e-14171
cerebral cortex7.73e-1325
pallium7.73e-1325
multi-tissue structure2.24e-11342
regional part of cerebral cortex3.46e-1122
anatomical cluster5.42e-11373
neocortex6.32e-1020
organ5.90e-07503
neural nucleus6.45e-079
nucleus of brain6.45e-079
basal ganglion6.54e-079
nuclear complex of neuraxis6.54e-079
aggregate regional part of brain6.54e-079
collection of basal ganglia6.54e-079
cerebral subcortex6.54e-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
CTCF#1066435.360256373075030.0064925092527670.0279940208838962
EBF1#187938.9064668465690.00141523283560980.0091622552763608
ESR1#2099220.51240219743630.003099741577095180.0163139442940054
RAD21#5885310.35503389545630.0009004912073565420.00665155960146473
RFX5#5993312.04791082719510.0005717246050312580.00485331594122243
SMC3#9126315.04493284493280.0002935825420371870.00309586703431156
TFAP2A#7020316.5186343730450.0002218033880766340.00248604035708688
TFAP2C#7022310.80922860986020.0007916746575753130.00616705523700366
TRIM28#10155318.59052504526250.0001555969297255280.00197309224667367



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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