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{{Coexpression_clusters
{
|full_id=C1662_Eosinophils_Dendritic_Neutrophils_Whole_renal_splenic_giant
|

Latest revision as of 11:49, 17 September 2013


Full id: C1662_Eosinophils_Dendritic_Neutrophils_Whole_renal_splenic_giant



Phase1 CAGE Peaks

Hg19::chr12:129308446..129308453,-p7@SLC15A4
Hg19::chr12:129308487..129308588,-p1@SLC15A4
Hg19::chr3:13057835..13057855,-p@chr3:13057835..13057855
-
Hg19::chr3:44552063..44552064,-p4@ZNF852
Hg19::chr6:42897306..42897321,+p5@CNPY3


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:0006857oligopeptide transport0.00350288472860002
GO:0015833peptide transport0.00401801483574708



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
leukocyte4.89e-56136
nongranular leukocyte2.35e-49115
hematopoietic stem cell9.68e-42168
angioblastic mesenchymal cell9.68e-42168
hematopoietic lineage restricted progenitor cell1.40e-39120
myeloid leukocyte1.61e-3872
hematopoietic cell2.49e-38177
classical monocyte4.22e-3842
CD14-positive, CD16-negative classical monocyte4.22e-3842
defensive cell5.71e-3648
phagocyte5.71e-3648
hematopoietic oligopotent progenitor cell7.71e-36161
hematopoietic multipotent progenitor cell7.71e-36161
monopoietic cell1.26e-3159
monocyte1.26e-3159
monoblast1.26e-3159
promonocyte1.26e-3159
macrophage dendritic cell progenitor3.65e-3061
myeloid lineage restricted progenitor cell6.66e-2766
granulocyte monocyte progenitor cell2.61e-2667
stuff accumulating cell7.85e-2187
myeloid cell1.63e-20108
common myeloid progenitor1.63e-20108
lymphocyte of B lineage7.49e-1624
pro-B cell7.49e-1624
lymphocyte2.60e-1453
common lymphoid progenitor2.60e-1453
granulocyte5.64e-148
intermediate monocyte8.25e-149
CD14-positive, CD16-positive monocyte8.25e-149
lymphoid lineage restricted progenitor cell1.72e-1352
nucleate cell1.72e-1355
mesenchymal cell7.76e-12354
motile cell1.09e-11386
connective tissue cell3.69e-11361
blood cell1.38e-0911
stem cell9.34e-09441
multi fate stem cell1.23e-07427
somatic stem cell1.30e-07433
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.37e-3298
blood island1.37e-3298
hemolymphoid system3.86e-29108
immune system2.61e-2593
bone marrow2.97e-2476
bone element1.62e-2182
skeletal element1.30e-1990
skeletal system2.09e-17100
lateral plate mesoderm1.58e-11203
connective tissue3.18e-11371
musculoskeletal system3.58e-07167


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)
MA0003.13.78382
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.11.45664
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.12.0635
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.14.94778
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.14.86996
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.11.55172
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.11.70569
MA0074.10.730989
MA0076.12.29573
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.11.52322
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.11.82062
MA0147.10.386018
MA0148.11.57313
MA0149.10.681935
MA0062.21.41923
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.20.30855
MA0137.21.20193
MA0104.20.858845
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.11.72541
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.03616
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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#90545.068961261570110.002709998091280770.0148900194999617
CHD2#110648.275218267293490.0004028373567101730.0038768826665549
E2F1#186943.925911371903460.007214984547106360.0298674450479702
EGR1#195843.990543275848110.0067800983001440.0287591051242279
ELF1#199754.258097958807540.0007142416939776840.0057261601502522
ELK4#200539.741408995080820.00212558656574340.0122865915065129
ETS1#211347.783008737761870.0005121035947688870.00443957726687705
FOS#235335.398773185336640.01153895317278740.0421871011136578
GABPB1#255345.654147068945740.001776696502096670.0109048193454674
MXI1#460135.976942977255580.008653004889366880.0329436853908059
NFKB1#479044.390450739355070.004707732692524960.0221953274952426
NFYA#4800311.05534841989830.001470892907644430.00941059693589048
NFYB#4801310.05587595212190.001938165606725460.0113866275412499
PAX5#507945.335652424942260.002223389586187790.0127741547470495
PBX3#5090313.14870761204650.0008860469322808430.00660230133850449
SIN3A#2594244.327107781452110.004977052855762880.0232395235482192
SP2#6668420.92282439507571.03516506540382e-050.000269269250973125
SREBF1#6720218.80233977619530.004335312729587370.0205769735577793
TAF1#687253.343046285745290.002394600090870310.0135190896205419
TCF12#693848.507571921749140.0003614215578492260.00361106917442029
THAP1#55145212.54765784114050.009528434667386530.0358867720240599
USF2#7392410.39375790805570.0001646179728687530.00202622704401175
YY1#752854.911170749853860.00034993140821360.00352493116728589
ZBTB33#10009212.66589001199250.009357016059651590.0353380125932578



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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