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{{Coexpression_clusters
{
|full_id=C613_CD4_CD19_CD8_Natural_CD14_immature_Peripheral
|

Latest revision as of 11:27, 17 September 2013


Full id: C613_CD4_CD19_CD8_Natural_CD14_immature_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:120514851..120514864,+p@chr10:120514851..120514864
+
Hg19::chr11:66445589..66445601,+p@chr11:66445589..66445601
+
Hg19::chr12:16035195..16035237,-p5@EPS8
Hg19::chr15:63796007..63796022,-p@chr15:63796007..63796022
-
Hg19::chr17:7386814..7386828,+p@chr17:7386814..7386828
+
Hg19::chr19:14116676..14116682,+p@chr19:14116676..14116682
+
Hg19::chr1:176176478..176176481,+p2@ENST00000456125
Hg19::chr1:179335173..179335190,+p4@AXDND1
Hg19::chr2:157198321..157198340,+p@chr2:157198321..157198340
+
Hg19::chr2:157198353..157198377,+p@chr2:157198353..157198377
+
Hg19::chr2:198318580..198318624,-p1@AK096309
Hg19::chr3:185655763..185655783,-p1@TRA2B
Hg19::chr5:40679504..40679537,+p3@PTGER4
Hg19::chr6:43192303..43192348,+p@chr6:43192303..43192348
+


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:0004957prostaglandin E receptor activity0.0246190848913119
GO:0030278regulation of ossification0.0246190848913119
GO:0004955prostaglandin receptor activity0.0246190848913119
GO:0046850regulation of bone remodeling0.0246190848913119
GO:0004954prostanoid receptor activity0.0246190848913119
GO:0004953icosanoid receptor activity0.0246190848913119
GO:0007173epidermal growth factor receptor signaling pathway0.0257868660157688
GO:0005070SH3/SH2 adaptor activity0.0334876079256093
GO:0060090molecular adaptor activity0.0349427208736638
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0349427208736638
GO:0019933cAMP-mediated signaling0.0349427208736638
GO:0001503ossification0.0349427208736638
GO:0031214biomineral formation0.0349427208736638
GO:0030674protein binding, bridging0.0349427208736638
GO:0046849bone remodeling0.0349427208736638
GO:0048771tissue remodeling0.0358204378027972
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0369769702662953
GO:0019935cyclic-nucleotide-mediated signaling0.0369769702662953
GO:0007166cell surface receptor linked signal transduction0.0477975200649953



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
leukocyte1.69e-54136
hematopoietic stem cell7.30e-50168
angioblastic mesenchymal cell7.30e-50168
hematopoietic cell3.27e-47177
hematopoietic oligopotent progenitor cell5.81e-45161
hematopoietic multipotent progenitor cell5.81e-45161
nongranular leukocyte2.06e-43115
hematopoietic lineage restricted progenitor cell8.25e-43120
classical monocyte2.14e-3242
CD14-positive, CD16-negative classical monocyte2.14e-3242
defensive cell1.66e-2548
phagocyte1.66e-2548
myeloid leukocyte3.38e-2572
granulocyte monocyte progenitor cell3.47e-2367
myeloid cell4.72e-23108
common myeloid progenitor4.72e-23108
macrophage dendritic cell progenitor3.98e-2161
lymphocyte1.03e-2053
common lymphoid progenitor1.03e-2053
lymphoid lineage restricted progenitor cell2.46e-2052
myeloid lineage restricted progenitor cell3.04e-2066
monopoietic cell9.36e-2059
monocyte9.36e-2059
monoblast9.36e-2059
promonocyte9.36e-2059
nucleate cell1.91e-1955
mesenchymal cell2.41e-17354
connective tissue cell1.34e-16361
motile cell2.38e-15386
stem cell6.19e-11441
multi fate stem cell2.01e-10427
somatic stem cell4.64e-10433
T cell8.47e-1025
pro-T cell8.47e-1025
stuff accumulating cell1.21e-0987
lymphocyte of B lineage1.77e-0924
pro-B cell1.77e-0924
native cell2.38e-08722
mature alpha-beta T cell3.43e-0818
alpha-beta T cell3.43e-0818
immature T cell3.43e-0818
mature T cell3.43e-0818
immature alpha-beta T cell3.43e-0818
B cell4.66e-0814
intermediate monocyte1.64e-079
CD14-positive, CD16-positive monocyte1.64e-079
Uber Anatomy
Ontology termp-valuen
bone marrow5.49e-2176
hematopoietic system6.30e-2198
blood island6.30e-2198
bone element6.78e-1982
immune system2.74e-1793
hemolymphoid system1.05e-16108
connective tissue4.09e-16371
skeletal element9.78e-1590
skeletal system7.62e-12100


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)
MA0003.10.426302
MA0004.12.12862
MA0006.10.906232
MA0007.10.260673
MA0009.10.695988
MA0014.10.856585
MA0017.10.181071
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.492785
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.499624
MA0050.10.73369
MA0051.11.685
MA0052.10.623986
MA0055.10.148782
MA0056.10
MA0057.11.99618
MA0058.12.44274
MA0059.11.72085
MA0060.10.564002
MA0061.11.27348
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.385025
MA0069.10.681911
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.10.942538
MA0074.10.358953
MA0076.11.14644
MA0077.10.65962
MA0078.10.447828
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.14098
MA0089.10
MA0090.10.223576
MA0091.10.278153
MA0092.10.247341
MA0093.12.81524
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.475507
MA0103.10.146091
MA0105.10.430023
MA0106.10.399649
MA0107.10.708233
MA0108.21.33623
MA0109.10
MA0111.10.660878
MA0113.10.414278
MA0114.10.339925
MA0115.10.929032
MA0116.10.354243
MA0117.10.732
MA0119.10.548507
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.11.17298
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.966693
MA0139.10.206516
MA0140.10.327488
MA0141.10.574537
MA0142.10.514195
MA0143.10.414436
MA0144.10.652118
MA0145.10.547424
MA0146.10.74748
MA0147.12.37497
MA0148.10.296708
MA0149.11.5426
MA0062.21.73596
MA0035.20.326883
MA0039.23.45695
MA0138.20.44894
MA0002.20.0708857
MA0137.20.504333
MA0104.21.96419
MA0047.20.388882
MA0112.20.78415
MA0065.20.846317
MA0150.10.624926
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.42076
MA0155.10.283527
MA0156.12.22453
MA0157.10.489002
MA0158.10
MA0159.10.730396
MA0160.10.30953
MA0161.10
MA0162.12.58965
MA0163.11.1565
MA0164.10.425415
MA0080.22.10447
MA0018.20.400879
MA0099.20.333432
MA0079.25.27144
MA0102.21.22472
MA0258.10.300766
MA0259.11.79733
MA0442.10



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
CCNT2#90573.168100788481320.002983097937573470.0158792948777898
E2F1#186982.804222408502470.002716619611129390.0149216911521375
E2F4#187465.429168706550470.0004158449263717840.00391229873573036
E2F6#1876103.583682665498134.45981311345876e-050.000790392706187883
EGR1#195893.206686560949370.0003889267057646490.00380506943544301
ELF1#1997103.041498542005380.0001960883233653430.00235773295002913
ELK4#200544.638766188133720.008733913817853870.0331815651226934
ETS1#211396.254203449987221.57751348151719e-066.00415198601216e-05
FOSL2#235544.837200172731910.007541622873992410.0310889895929305
GABPB1#255384.038676477818380.0002160368143870840.0024775083845144
GTF2B#295936.845106414498050.008614109848639840.0328147438897759
GTF2F1#296265.459854661467560.0004033133552769910.00388039092692526
HEY1#23462123.462952322662042.86301377032512e-069.8423401961483e-05
HMGN3#932484.673455841914627.53694136401289e-050.00116684052640994
IRF1#365984.364093573465090.0001238143250234230.00165084186022231
JUN#372554.468867568691550.00352745885080830.0179089142443035
JUNB#372636.559421284247390.009679313046712050.0364221861028845
JUND#372762.997713117944730.009116463920820550.0344943980663205
MAX#414994.148071398647444.88080712048191e-050.000847177355585857
MXI1#460185.692326645005311.76881691091529e-050.000403700763459532
MYC#4609124.476241604236631.49722896143429e-078.42960083575398e-06
NRF1#489976.105139723855455.0447325218961e-050.000859629335706162
POLR2A#5430142.147453176558072.25331953374171e-050.000492640650584991
POU2F2#545253.252187163479470.01362351556019460.0480700814754269
REST#597864.135726592626290.001776161327137930.0109085864654489
RFX5#599354.302825295426820.004160224493762290.0198261321425526
SIN3A#25942103.863489090582242.23981931004689e-050.000490099494913026
SMARCB1#659845.215061651759260.005781759737825980.0259985019055717
SP1#666772.849190689070450.005537931113228910.0250704806040102
TAF1#6872133.104257265334911.55079831716319e-065.91108851993454e-05
TBP#6908143.706770687096391.08014255397772e-088.13330989148374e-07
TCF12#693875.317232451093210.0001225526264572570.001651519194138
TFAP2C#702253.86043878923580.006637273182023020.0283038738253768
YY1#752882.806383285630770.002702639654839410.0148660126882484
ZBTB7A#5134184.201091033071940.0001628644135476470.00202637556427242
ZNF263#1012763.523646415861720.004061029105107940.0194260898048078



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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