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Coexpression cluster:C4641: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!7.24e-40!115;UBERON:0005743!3.98e-23!86;UBERON:0001017!8.29e-23!82;UBERON:0000073!1.36e-21!94;UBERON:0001016!1.36e-21!94;UBERON:0001049!1.69e-21!57;UBERON:0005068!1.69e-21!57;UBERON:0006241!1.69e-21!57;UBERON:0007135!1.69e-21!57;UBERON:0003080!6.66e-20!42;UBERON:0002780!3.10e-19!41;UBERON:0001890!3.10e-19!41;UBERON:0006240!3.10e-19!41;UBERON:0002616!1.18e-18!59;UBERON:0000955!2.81e-18!69;UBERON:0006238!2.81e-18!69;UBERON:0003075!1.46e-16!86;UBERON:0007284!1.46e-16!86;UBERON:0002346!1.83e-16!90;UBERON:0001869!4.96e-16!32;UBERON:0001893!5.20e-16!34;UBERON:0002020!5.77e-16!34;UBERON:0003528!5.77e-16!34;UBERON:0002791!1.88e-15!33;UBERON:0003056!1.12e-14!61;UBERON:0002619!2.35e-13!22;UBERON:0001950!9.27e-13!20;UBERON:0000956!1.59e-12!25;UBERON:0000203!1.59e-12!25;UBERON:0000153!2.81e-10!129;UBERON:0007811!2.81e-10!129;UBERON:0000033!6.27e-10!123;UBERON:0000924!6.34e-09!173;UBERON:0006601!6.34e-09!173;UBERON:0004121!8.69e-09!169;UBERON:0001986!6.48e-07!18;UBERON:0004638!6.48e-07!18;UBERON:0004852!6.48e-07!18
|ontology_enrichment_uberon=UBERON:0007023!7.24e-40!115;UBERON:0005743!3.98e-23!86;UBERON:0001017!8.29e-23!82;UBERON:0000073!1.36e-21!94;UBERON:0001016!1.36e-21!94;UBERON:0001049!1.69e-21!57;UBERON:0005068!1.69e-21!57;UBERON:0006241!1.69e-21!57;UBERON:0007135!1.69e-21!57;UBERON:0003080!6.66e-20!42;UBERON:0002780!3.10e-19!41;UBERON:0001890!3.10e-19!41;UBERON:0006240!3.10e-19!41;UBERON:0002616!1.18e-18!59;UBERON:0000955!2.81e-18!69;UBERON:0006238!2.81e-18!69;UBERON:0003075!1.46e-16!86;UBERON:0007284!1.46e-16!86;UBERON:0002346!1.83e-16!90;UBERON:0001869!4.96e-16!32;UBERON:0001893!5.20e-16!34;UBERON:0002020!5.77e-16!34;UBERON:0003528!5.77e-16!34;UBERON:0002791!1.88e-15!33;UBERON:0003056!1.12e-14!61;UBERON:0002619!2.35e-13!22;UBERON:0001950!9.27e-13!20;UBERON:0000956!1.59e-12!25;UBERON:0000203!1.59e-12!25;UBERON:0000153!2.81e-10!129;UBERON:0007811!2.81e-10!129;UBERON:0000033!6.27e-10!123;UBERON:0000924!6.34e-09!173;UBERON:0006601!6.34e-09!173;UBERON:0004121!8.69e-09!169;UBERON:0001986!6.48e-07!18;UBERON:0004638!6.48e-07!18;UBERON:0004852!6.48e-07!18
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00905936,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.0791124,0.0330727,0.00956472,0.219556,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,0.0376172,0.0286025,2.02725e-05,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.00836526,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.109194,0.128564,0.131452,0.112518,0.0226843,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.0122266,0.655293,0.21727,0.289306,0.119215,0.00138836,0.00108376,0.0088427,0.057571,0.047591,0.0143259,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.000216899,2.32492e-07,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.0158019,0.104948,0.221645,0.057168,0.234298,0.0759837,0.000415994,0.152372,0.0203723,0.218271,0.101607,0.060512,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.034431,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.00352872,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.000886556,0.188651,0.0813902,0.184948,0.156261,0.311847,0.0001026,0.0590944,0.247324,0.178389,0.218229,0.231073,0.0161946,0.0743925,0.0360851,0.0998546,0.131093,0.0434602,0.133616,0.103051,0.0115948,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.057779,0.643768,0.00272579,5.79979e-05,0.390366,0.48809,0.50058,0.443185,0.522904,4.90206e-08,5.34955e-09,0.227104,0.0380245,0.00310917,0.38649,0.284625,0.00583062,0.00143312,0.00228337,0.28907,0.164197,0.0252589,0.287881,0.574635,0.478174,0.336276,0.000498078,0.258219,0.446557,0.243383,4.14881e-06,0.390974,0.000456298,0.00120937,0.161598,0.000101989,0.0868402,0.496032,4.65435e-05,0.0805771,5.07251e-06,0.477353,0.00492096,9.39021e-05,0.000153842,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.0997241,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.00162521,0.314429,0.00115141,0.282286,0.000180531,0.616388,0.408413,0.516511,0.0073454,0.656109,0.33942,0.0700181,0.387276,0.522605,1.15611e-06,0.537348,0.222037,0.416621,0.416292,0.128937,0.00246111,0.215157,0.204817,0.122646,0.138871,0.027191,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.0805711,0.00101302,0.408861,0.365487,0.178743,0.0140668,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.637444,0.00618487,0.00285094,0.371414,0.0527347,0.303709,0.495883,0.0135408,0.508064,0.250964,0.383276,0.457886,0.504711,0.0262575,0.509064,0.196976,0.191517,0.463751,0.00258603,0.307334,0.000443066,0.283463,0.201728,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.0283414,0.359231,0.339729,0.197805,0.608187,0.0870376,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.0424553,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.00329437,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.00215229,0.222977,0.00893033,0.0542164,0.21801,0.0211771,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.0233967,0.0335483,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.00242972,0.162145,0.228955,0.0151141,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.0377094,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.00106131,0.0969345,0.202137,0.310405,0.00467879,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.0025753,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.00569858,0.253509,0.177664,0.28365,0.0385243,0.131761,0.160658,0.206239,0.19924,0.28689,0.00267717,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.28172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}}
}}

Revision as of 14:16, 5 September 2012


Full id: C4641_mature_breast_Whole_Burkitt_pineal_adipose_chronic



Phase1 CAGE Peaks

Hg19::chr7:106685105..106685126,+p2@PRKAR2B
Hg19::chr7:106685133..106685186,+p1@PRKAR2B
Hg19::chr7:106685220..106685231,+p4@PRKAR2B


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>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism7.24e-40115
central nervous system8.29e-2382
regional part of nervous system1.36e-2194
nervous system1.36e-2194
neural tube1.69e-2157
neural rod1.69e-2157
future spinal cord1.69e-2157
neural keel1.69e-2157
anterior neural tube6.66e-2042
regional part of forebrain3.10e-1941
forebrain3.10e-1941
future forebrain3.10e-1941
regional part of brain1.18e-1859
brain2.81e-1869
future brain2.81e-1869
neural plate1.46e-1686
presumptive neural plate1.46e-1686
neurectoderm1.83e-1690
cerebral hemisphere4.96e-1632
telencephalon5.20e-1634
gray matter5.77e-1634
brain grey matter5.77e-1634
regional part of telencephalon1.88e-1533
pre-chordal neural plate1.12e-1461
regional part of cerebral cortex2.35e-1322
neocortex9.27e-1320
cerebral cortex1.59e-1225
pallium1.59e-1225
anterior region of body2.81e-10129
craniocervical region2.81e-10129
head6.27e-10123
ectoderm6.34e-09173
presumptive ectoderm6.34e-09173
ectoderm-derived structure8.69e-09169
endothelium6.48e-0718
blood vessel endothelium6.48e-0718
cardiovascular system endothelium6.48e-0718


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
ATF3#467322.46317452600878.81932387510763e-050.00130022778965608
CCNT2#90536.336201576962630.003930750035764890.0191074518494414
CHD2#1106310.34402283411690.0009033701102746880.00662689267029417
CTCF#1066435.360256373075030.0064925092527670.0281182323802502
E2F1#186934.907389214879320.008460985347239390.032755934636184
E2F4#1874312.66806031528440.0004917987006298980.00438849662466558
E2F6#187635.017155731697390.00791769806886330.0324179264785171
EGR1#195834.988179094810140.008056488137383440.0322367558553385
ELF1#199734.258097958807540.01295179875054610.0464804106146754
EP300#203336.77394172622320.003216880500103790.016838802252924
HDAC2#3066313.41562023662630.0004140761399857210.00393393049976974
HMGN3#932438.178547723350590.001827766942164210.0109161177830782
IRF1#365937.63716375356390.002244692747297240.0128703522281074
JUND#372736.994663941871030.002921845042734990.0157637449332679
MAX#414936.452555509007120.003721913834265510.0187349604268775
MXI1#460139.96157162875930.001011470541259020.00723194166211755
NRF1#4899312.21027944771090.0005492172401020010.00473303897508152
RAD21#5885310.35503389545630.0009004912073565420.00668227946604447
SIN3A#2594235.408884726815140.006318961977991520.027820001265469
USF1#739136.361499277207960.00388404057290560.0191107751528167
USF2#7392312.99219738506960.0004558979393427810.00423080903563362
YY1#752834.911170749853860.008441455341808260.0331111377767262



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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