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Difference between revisions of "Coexpression cluster:C3377"

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|full_id=C3377_CD14_CD4_acute_immature_esophagus_NK_CD14CD16
 
|full_id=C3377_CD14_CD4_acute_immature_esophagus_NK_CD14CD16
 
|id=C3377
 
|id=C3377
|ontology_enrichment_celltype=CL:0002057!7.34e-20!42;CL:0002009!2.64e-18!65;CL:0002194!2.55e-17!63;CL:0000576!2.55e-17!63;CL:0000040!2.55e-17!63;CL:0000559!2.55e-17!63;CL:0000860!3.00e-16!45;CL:0000557!3.73e-15!71;CL:0000766!6.13e-14!76;CL:0000839!1.69e-13!70;CL:0002087!3.04e-13!119;CL:0000738!1.92e-12!140;CL:0002031!1.84e-11!124;CL:0000791!1.27e-09!18;CL:0000789!1.27e-09!18;CL:0002420!1.27e-09!18;CL:0002419!1.27e-09!18;CL:0000790!1.27e-09!18;CL:0000763!3.75e-07!112;CL:0000049!3.75e-07!112;CL:0000037!6.68e-07!172;CL:0000566!6.68e-07!172
+
|ontology_enrichment_celltype=CL:0000473!5.01e-24!48;CL:0000234!5.01e-24!48;CL:0002009!1.66e-21!61;CL:0000860!1.53e-20!42;CL:0002057!1.53e-20!42;CL:0002194!1.60e-20!59;CL:0000576!1.60e-20!59;CL:0000040!1.60e-20!59;CL:0000559!1.60e-20!59;CL:0000557!5.02e-18!67;CL:0000839!2.51e-16!66;CL:0000766!4.97e-16!72;CL:0002087!9.96e-16!115;CL:0000325!2.20e-14!87;CL:0000738!3.28e-14!136;CL:0002031!1.06e-13!120;CL:0000791!1.25e-09!18;CL:0000789!1.25e-09!18;CL:0002420!1.25e-09!18;CL:0002419!1.25e-09!18;CL:0000790!1.25e-09!18;CL:0000763!2.78e-09!108;CL:0000049!2.78e-09!108;CL:0000037!5.27e-09!168;CL:0000566!5.27e-09!168;CL:0002032!1.27e-08!161;CL:0000837!1.27e-08!161;CL:0000988!1.85e-07!177
 
|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.90e-22!115;UBERON:0002193!5.71e-19!112;UBERON:0002390!5.02e-18!102;UBERON:0003061!5.02e-18!102;UBERON:0002405!2.06e-15!115;UBERON:0002371!3.42e-13!80;UBERON:0001474!1.55e-10!86;UBERON:0004765!4.03e-09!101;UBERON:0001434!4.03e-09!101
+
|ontology_enrichment_uberon=UBERON:0007023!4.14e-21!114;UBERON:0002193!5.90e-21!108;UBERON:0002390!3.40e-20!98;UBERON:0003061!3.40e-20!98;UBERON:0002405!2.81e-17!93;UBERON:0002371!4.38e-15!76;UBERON:0001474!1.65e-12!82;UBERON:0004765!1.22e-11!90;UBERON:0001434!1.00e-10!100;UBERON:0003081!4.69e-07!203
 
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460845226801677!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167123206760354!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00580111175073279!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107093815128724!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436362180039532!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000849805383947738!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00390339362613672!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443562758061199!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245844169797498!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108920305344649!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00641801418882482!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00612384974447526
 
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460845226801677!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167123206760354!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00580111175073279!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107093815128724!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436362180039532!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000849805383947738!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00390339362613672!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443562758061199!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245844169797498!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108920305344649!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00641801418882482!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00612384974447526
 
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07043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.00327141,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.00102636,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.00628729,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.0458068,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.112518,0.00327218,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.0926491,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.00224624,0.291114,0.0355833,0.125606,0.00102956,0.43617,0.936279,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,6.10604e-05,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.00148023,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.0122477,0.194941,0.218271,0.101607,0.327067,0.172982,0.00886538,0.151597,0.0626744,1.06249e-07,0.148574,0.504592,0.155821,6.54495e-05,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.0200941,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.000263756,0.112651,0.186638,0.174776,0.0948451,0.0384217,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0125264,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.619906,0.0360851,0.412187,0.00899487,0.0434602,0.133616,0.418146,0.36927,0.0227305,0.407369,3.69044e-07,0.00858901,0.0210947,0.000119767,0.10748,0.120472,0.197484,0.396996,0.36145,0.0966095,0.381071,0.057779,0.643768,0.0198622,0.722159,0.0140037,0.48809,0.50058,0.443185,0.0391928,0.875915,0.871256,0.227104,0.0380245,0.0734371,0.38649,0.000401783,0.000799065,0.192225,0.729153,0.00513616,0.164197,0.00379441,0.287881,3.14651e-05,0.0283889,6.86351e-05,0.132529,0.258219,0.446557,0.032364,0.777351,0.00170027,0.73485,0.109758,0.161598,0.405056,0.0868402,0.00534461,0.799185,0.37357,0.454657,0.477353,0.199161,0.746954,0.00415823,0.20342,0.00158025,0.00171127,0.0505073,0.25656,0.425963,0.00100853,0.00154995,0.156104,0.000526011,0.411941,0.0961477,0.00677445,0.354789,0.163828,0.0289012,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.78,0.616388,0.000215097,0.516511,0.000699859,0.656109,0.000885969,0.0700181,0.0136291,0.522605,0.802166,0.0433137,0.222037,0.102227,7.53331e-13,0.462712,0.148994,3.41694e-05,0.204817,0.452428,0.138871,0.00105709,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.0628556,0.00137548,0.00701509,0.408861,0.365487,0.00116224,0.0889149,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.0830022,0.305885,0.241132,0.0795725,0.30666,0.0516603,0.0323359,0.386538,0.508064,0.250964,1.17227e-05,0.000432158,0.0344603,0.220231,0.509064,0.196976,0.191517,0.0254647,0.235208,0.307334,0.459728,0.283463,0.563586,0.000528727,0.0151656,0.273281,0.0780405,2.19858e-05,0.0858306,0.47795,0.359231,0.0656472,0.197805,0.608187,0.387069,0.0627969,0.52832,0.00579439,0.000613177,0.205413,0.17639,0.0779009,2.27924e-05,0.205298,0.0337138,7.87273e-11,0.036838,0.188263,0.0719199,0.264884,0.0139948,1.97047e-12,0.163057,0.219428,0.0233135,0.0900729,0.0953646,0.166124,0.252184,0.012591,0.255516,0.20753,0.119514,0.179412,0.00141426,0.220904,0.222977,0.341681,0.00651011,0.21801,0.0211771,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.00112112,0.226869,0.00455899,0.000111542,0.131118,0.20837,0.0335483,0.222339,0.0673329,0.20847,0.266544,0.000263373,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,8.62798e-07,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.00200124,0.158479,0.220319,0.195218,0.124213,0.259632,2.52161e-06,0.180606,0.000773769,0.00351525,0.150733,0.217112,0.123917,0.00121059,0.00123184,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.0331281,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.00649151,0.280943,0.0257454,0.0822373,0.202065,0.00591081,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.00186843,0.187731,0.0025753,0.00132285,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.00414049,0.0367455,0.13497,0.204393,1.91331e-06,0.00499908,0.000980315,0.141729,0.0037817,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,1.7636e-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}}
 
}}

Revision as of 06:03, 19 October 2012


Full id: C3377_CD14_CD4_acute_immature_esophagus_NK_CD14CD16



Phase1 CAGE Peaks

  Short description
Hg19::chr13:48987196..48987207,- p3@LPAR6
Hg19::chr13:48987228..48987239,- p2@LPAR6
Hg19::chr13:48987241..48987260,- p1@LPAR6


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
defensive cell5.01e-2448
phagocyte5.01e-2448
macrophage dendritic cell progenitor1.66e-2161
classical monocyte1.53e-2042
CD14-positive, CD16-negative classical monocyte1.53e-2042
monopoietic cell1.60e-2059
monocyte1.60e-2059
monoblast1.60e-2059
promonocyte1.60e-2059
granulocyte monocyte progenitor cell5.02e-1867
myeloid lineage restricted progenitor cell2.51e-1666
myeloid leukocyte4.97e-1672
nongranular leukocyte9.96e-16115
stuff accumulating cell2.20e-1487
leukocyte3.28e-14136
hematopoietic lineage restricted progenitor cell1.06e-13120
mature alpha-beta T cell1.25e-0918
alpha-beta T cell1.25e-0918
immature T cell1.25e-0918
mature T cell1.25e-0918
immature alpha-beta T cell1.25e-0918
myeloid cell2.78e-09108
common myeloid progenitor2.78e-09108
hematopoietic stem cell5.27e-09168
angioblastic mesenchymal cell5.27e-09168
hematopoietic oligopotent progenitor cell1.27e-08161
hematopoietic multipotent progenitor cell1.27e-08161
hematopoietic cell1.85e-07177
Uber Anatomy
Ontology termp-valuen
adult organism4.14e-21114
hemolymphoid system5.90e-21108
hematopoietic system3.40e-2098
blood island3.40e-2098
immune system2.81e-1793
bone marrow4.38e-1576
bone element1.65e-1282
skeletal element1.22e-1190
skeletal system1.00e-10100
lateral plate mesoderm4.69e-07203


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ELF1#199734.258097958807540.01295179875054610.0460845226801677
EP300#203336.77394172622320.003216880500103790.0167123206760354
FOXA1#3169311.08141974938550.000734755275698670.00580111175073279
FOXA2#3170324.63046375266526.68983856509345e-050.00107093815128724
GATA2#2624312.7449317335540.0004829527704283790.00436362180039532
GATA3#2625327.2365163572064.94721007899563e-050.000849805383947738
HDAC2#3066313.41562023662630.0004140761399857210.00390339362613672
JUN#3725312.51282919233630.0005103313992726250.00443562758061199
SP1#666735.69838137814090.005403962701712170.0245844169797498
SPI1#668838.204323508522730.001810593189410520.0108920305344649
STAT3#6774310.51946499715420.0008589184530415310.00641801418882482
TCF7L2#6934310.77017656313730.0008003181298398380.00612384974447526



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.