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Coexpression cluster:C4752: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!4.30e-28!102;UBERON:0003061!4.30e-28!102;UBERON:0002371!2.90e-24!80;UBERON:0002193!4.76e-23!112;UBERON:0001474!6.85e-21!86;UBERON:0004765!2.28e-16!101;UBERON:0001434!2.28e-16!101;UBERON:0002204!2.91e-13!167;UBERON:0002405!4.29e-13!115;UBERON:0003081!7.40e-12!216;UBERON:0002384!1.25e-07!375
|ontology_enrichment_uberon=UBERON:0002390!4.30e-28!102;UBERON:0003061!4.30e-28!102;UBERON:0002371!2.90e-24!80;UBERON:0002193!4.76e-23!112;UBERON:0001474!6.85e-21!86;UBERON:0004765!2.28e-16!101;UBERON:0001434!2.28e-16!101;UBERON:0002204!2.91e-13!167;UBERON:0002405!4.29e-13!115;UBERON:0003081!7.40e-12!216;UBERON:0002384!1.25e-07!375
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327948357276057!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324548243107663!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322688998880226!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465187739771746!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168573899924907!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000679628701243626!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109298684038184!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.0063219464978354!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249675835819526!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00619292259475007
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237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.000107101,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.0355977,0.0154037,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.02609,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.0470027,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.0254773,0.190048,0.00899422,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00681584,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.00264443,1.8725e-06,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.300597,0.00260609,0.223874,0.291114,0.0355833,0.125606,0.175094,0.00352878,0.000141874,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.0203723,0.218271,0.101607,0.060512,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.15663,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.00326415,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.000902392,0.09066,0.00213659,0.166967,0.188651,0.0813902,0.0182671,0.156261,0.311847,0.0001026,0.0590944,0.247324,0.178389,0.218229,0.231073,0.0972686,0.0743925,0.0360851,0.0021796,1.45218e-05,0.0434602,0.133616,0.0177337,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.0189483,0.448797,0.197484,0.396996,0.36145,0.0966095,0.381071,0.057779,0.643768,0.11074,0.000369536,0.390366,0.48809,0.50058,0.443185,0.522904,2.0991e-06,0.00127936,0.227104,0.166658,0.000486104,0.38649,0.00488219,0.156746,0.04783,9.48418e-06,0.28907,0.164197,0.0252589,0.287881,0.574635,0.478174,0.336276,0.132529,0.258219,0.0222932,0.243383,0.00448654,0.0889613,7.41696e-05,0.00650842,0.161598,0.000599447,0.021206,0.150692,0.00136122,0.37357,0.00106614,0.477353,0.00104348,9.39021e-05,0.0629574,0.20342,0.00158025,0.20558,0.300504,0.25656,0.0189087,0.349197,0.383291,0.156104,0.141318,0.0168417,0.0961477,0.055627,0.354789,0.163828,0.230581,0.120226,0.00486063,0.0101317,0.314429,0.181415,0.282286,0.0192486,0.24884,0.408413,0.516511,0.322213,0.0931134,0.33942,0.0700181,0.387276,0.169614,0.00143411,0.537348,0.222037,0.416621,0.0174635,0.0252635,0.00246111,0.0118519,0.204817,0.452428,0.138871,0.103502,0.166905,0.19783,0.0833851,0.056391,0.48065,0.0163316,0.0628556,0.0120568,0.523625,0.408861,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.269604,0.305885,0.241132,0.371414,0.30666,0.303709,0.0323359,0.0867777,0.508064,0.250964,0.383276,0.0243456,0.504711,0.220231,0.159791,0.196976,0.191517,0.463751,5.00877e-05,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.0780405,0.275089,0.384593,0.0283414,0.359231,0.339729,0.197805,0.00278185,0.387069,0.332774,0.52832,0.299887,0.266492,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.0260582,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,2.65303e-06,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,1.84405e-05,0.113092,0.145701,0.229428,0.162145,0.00241368,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.00160819,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.000773769,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.00371613,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,1.16102e-05,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.000206969,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.000455851,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.0015491,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.00135479,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 13:56, 5 September 2012


Full id: C4752_Mast_Basophils_CD8_Neutrophils_CD34_Eosinophils_Natural



Phase1 CAGE Peaks

Hg19::chr8:38758764..38758787,+p5@PLEKHA2
Hg19::chr8:38758806..38758831,+p6@PLEKHA2
Hg19::chr8:38758845..38758875,+p3@PLEKHA2


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>

Cell Type
Ontology termp-valuen
leukocyte4.64e-47140
nongranular leukocyte2.51e-40119
hematopoietic lineage restricted progenitor cell8.10e-39124
hematopoietic stem cell3.88e-37172
angioblastic mesenchymal cell3.88e-37172
hematopoietic oligopotent progenitor cell2.11e-34165
hematopoietic multipotent progenitor cell2.11e-34165
hematopoietic cell2.54e-33182
myeloid leukocyte3.98e-3076
granulocyte monocyte progenitor cell1.63e-2571
myeloid lineage restricted progenitor cell1.36e-2270
macrophage dendritic cell progenitor2.17e-2265
monopoietic cell2.20e-2263
monocyte2.20e-2263
monoblast2.20e-2263
promonocyte2.20e-2263
classical monocyte6.78e-2245
CD14-positive, CD16-negative classical monocyte2.20e-2042
myeloid cell4.34e-18112
common myeloid progenitor4.34e-18112
lymphocyte9.09e-1653
common lymphoid progenitor9.09e-1653
lymphoid lineage restricted progenitor cell2.02e-1552
mature alpha-beta T cell1.37e-0918
alpha-beta T cell1.37e-0918
immature T cell1.37e-0918
mature T cell1.37e-0918
immature alpha-beta T cell1.37e-0918
B cell2.17e-0814
lymphocyte of B lineage8.80e-0824
pro-B cell8.80e-0824
T cell2.82e-0725
pro-T cell2.82e-0725
connective tissue cell4.16e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.30e-28102
blood island4.30e-28102
bone marrow2.90e-2480
hemolymphoid system4.76e-23112
bone element6.85e-2186
skeletal element2.28e-16101
skeletal system2.28e-16101
musculoskeletal system2.91e-13167
immune system4.29e-13115
lateral plate mesoderm7.40e-12216
connective tissue1.25e-07375


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
E2F1#186934.907389214879320.008460985347239390.0327948357276057
E2F6#187635.017155731697390.00791769806886330.0324548243107663
EGR1#195834.988179094810140.008056488137383440.0322688998880226
ELF1#199734.258097958807540.01295179875054610.0465187739771746
EP300#203336.77394172622320.003216880500103790.0168573899924907
ESR1#2099330.76860329615453.43136389821584e-050.000679628701243626
HMGN3#932438.178547723350590.001827766942164210.0109298684038184
TCF12#6938310.63446490218640.0008313523990202070.0063219464978354
TFAP2A#7020316.5186343730450.0002218033880766340.00249675835819526
TFAP2C#7022310.80922860986020.0007916746575753130.00619292259475007



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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