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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:31, 17 September 2013


Full id: C815_Basophils_Eosinophils_CD14_Mast_Peripheral_CD34_CD14CD16



Phase1 CAGE Peaks

Hg19::chr12:13253999..13254015,-p@chr12:13253999..13254015
-
Hg19::chr14:75725551..75725560,-p@chr14:75725551..75725560
-
Hg19::chr14:75725567..75725572,-p@chr14:75725567..75725572
-
Hg19::chr14:75725579..75725612,-p@chr14:75725579..75725612
-
Hg19::chr14:75725628..75725642,-p@chr14:75725628..75725642
-
Hg19::chr14:75743949..75743996,+p@chr14:75743949..75743996
+
Hg19::chr19:6057282..6057313,-p@chr19:6057282..6057313
-
Hg19::chr2:196933270..196933275,+p@chr2:196933270..196933275
+
Hg19::chr6:159463538..159463554,+p@chr6:159463538..159463554
+
Hg19::chr9:36152083..36152105,+p@chr9:36152083..36152105
+


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
classical monocyte1.71e-4142
CD14-positive, CD16-negative classical monocyte1.71e-4142
leukocyte2.69e-37136
myeloid leukocyte4.35e-3772
defensive cell5.51e-3448
phagocyte5.51e-3448
hematopoietic stem cell8.86e-33168
angioblastic mesenchymal cell8.86e-33168
granulocyte monocyte progenitor cell1.58e-3167
hematopoietic cell2.21e-29177
macrophage dendritic cell progenitor3.11e-2961
hematopoietic oligopotent progenitor cell4.69e-29161
hematopoietic multipotent progenitor cell4.69e-29161
myeloid cell2.29e-28108
common myeloid progenitor2.29e-28108
monopoietic cell1.02e-2759
monocyte1.02e-2759
monoblast1.02e-2759
promonocyte1.02e-2759
myeloid lineage restricted progenitor cell1.08e-2766
hematopoietic lineage restricted progenitor cell2.16e-27120
nongranular leukocyte4.06e-27115
mesenchymal cell4.84e-16354
connective tissue cell5.14e-16361
stuff accumulating cell1.30e-1587
motile cell1.81e-12386
intermediate monocyte5.84e-119
CD14-positive, CD16-positive monocyte5.84e-119
granulocyte5.10e-108
multi fate stem cell5.33e-09427
stem cell7.04e-09441
somatic stem cell2.11e-08433
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.33e-3498
blood island3.33e-3498
bone marrow7.48e-3176
hemolymphoid system1.20e-28108
bone element3.99e-2882
skeletal element6.71e-2690
immune system2.67e-2393
skeletal system4.79e-22100
connective tissue2.25e-15371
lateral plate mesoderm3.71e-10203


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)
MA0003.11.34002
MA0004.11.75693
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.954641
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.11.75547
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.13.59645
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.12.13887
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.00880943
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.14.61139
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.918839
MA0093.11.93559
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.12.12449
MA0106.10.516528
MA0107.10.529721
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.11.02702
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.716757
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.491079
MA0145.10.602634
MA0146.11.46534
MA0147.10.184931
MA0148.12.74942
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.520808
MA0138.20.569505
MA0002.20.407187
MA0137.20.710884
MA0104.20.845907
MA0047.22.17709
MA0112.20.904106
MA0065.20.0371828
MA0150.10.845871
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.0494985
MA0155.12.72503
MA0156.10.257809
MA0157.11.4867
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.908343
MA0163.10.299639
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.603497
MA0102.21.36707
MA0258.10.919347
MA0259.10.560522
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
ATF3#46748.98526981040350.0006636746018777640.00542656476516964
BHLHE40#8553417.9487254187914.64476779317696e-050.00081501159870902
BRCA1#67248.07369225728950.0009931821541010780.00712802027158896
CCNT2#90553.168100788481320.01227157669794290.0444825488947821
CEBPB#105175.579803338077374.14051761029175e-050.00075166264331872
E2F1#186962.944433528927590.007015119886153280.0296344337576331
E2F4#187456.334030157642220.0005501567218568720.00469887290431877
E2F6#187673.512009012188170.0008453950419482970.00637304841822132
EGR1#195862.992907456886080.006446587185075730.028012278719456
ELF1#199783.406478367046030.0002607995998237460.00279532526744583
EP300#203374.741759208356240.0001211445349442930.00164165227521046
ESR1#2099412.30744131846180.0001999674803985190.00240023028219066
FOXA1#316955.540709874692730.001021651775689810.00724619964694523
FOXA2#3170512.31523187633262.33853114552725e-050.000510095769230829
GTF2F1#296245.095864350703060.00541638888230090.0245671084199871
HMGN3#932454.08927386167530.004038023271587280.0193346374684258
JUN#372578.758980434635432.00832209907879e-067.34408794487709e-05
JUNB#3726412.24425306392850.0002039607414596510.00242089508777185
JUND#372764.196798365122620.001065203456546050.00752443583349431
MAFF#23764422.52614259597811.91315680697685e-050.000433235437475834
MAFK#7975513.5503665689151.4731115171922e-050.000349580308439074
MAX#414995.807299958106414.43335817213899e-072.11326104125981e-05
MXI1#460176.973100140131519.35179885105888e-060.000248965720164603
MYC#460963.133369122965640.005077423268455520.0236300079646284
NFYA#480047.370232279932210.001397112769899070.0090900237089141
PAX5#507974.668695871824480.0001341235735206540.0017593232724094
PBX3#509048.765805074697650.000728667835365060.00581014964557119
POLR2A#543091.932707858902260.005980089183606110.0268118199642242
POU2F2#545265.463674434645510.0002482209573289410.00267809385976005
RFX5#599356.023955413597550.0006945114068748440.00559719706941908
SIN3A#2594273.786219308770590.0005225362319000430.00452663914427742
SMARCB1#659847.301086312462970.001447103644365430.0092777199210486
SPI1#668864.922594105113640.0004434197902305250.00412895145077441
SREBF1#6720628.2035096642931.80211605019971e-081.2989040591222e-06
STAT3#677477.363625498007976.48369150656884e-060.000191123414409975
TAF1#687272.34013240002170.01040839844348330.0386380438273601
TAF7#687944.573227761969570.007980040641138020.0322621245894714
TCF12#693866.380678941311850.0001037697574830750.00145081789849731
TFAP2A#702046.607453749217980.002096541917954080.0121247434170888
TFAP2C#702277.566460026902165.39952747293911e-060.000164841055172841
THAP1#55145412.54765784114050.0001856500560886790.00224723066850319
USF1#739163.816899566324770.001780928663791640.0109282261291267
USF2#739245.196878954027840.005046003840154460.023505780332823



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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