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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.106236511321066,-

Latest revision as of 11:36, 17 September 2013


Full id: C1025_Mast_lung_pineal_pituitary_cerebellum_Neutrophils_CD14



Phase1 CAGE Peaks

Hg19::chr13:33112899..33112948,-p1@N4BP2L2
Hg19::chr1:104068562..104068632,+p2@RNPC3
Hg19::chr22:38902300..38902322,-p1@DDX17
Hg19::chr22:38902325..38902347,-p2@DDX17
Hg19::chr2:135676381..135676435,+p1@CCNT2
Hg19::chr3:50126345..50126401,+p1@RBM5
Hg19::chr5:178054014..178054096,-p1@CLK4
Hg19::chr6:170615819..170615877,+p1@FAM120B


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:0006396RNA processing0.00680576209767547
GO:0003723RNA binding0.0213310656543628
GO:0005634nucleus0.0294399056100721
GO:0000074regulation of progression through cell cycle0.031184768323312
GO:0051726regulation of cell cycle0.031184768323312
GO:0016070RNA metabolic process0.0404000397154515
GO:0000166nucleotide binding0.0404000397154515
GO:0043283biopolymer metabolic process0.0404000397154515
GO:0008186RNA-dependent ATPase activity0.0410818184990109
GO:0022402cell cycle process0.0410818184990109
GO:0003724RNA helicase activity0.0410818184990109
GO:0043231intracellular membrane-bound organelle0.0410818184990109
GO:0043227membrane-bound organelle0.0410818184990109



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
leukocyte4.75e-29136
hematopoietic stem cell7.75e-28168
angioblastic mesenchymal cell7.75e-28168
hematopoietic oligopotent progenitor cell2.55e-26161
hematopoietic multipotent progenitor cell2.55e-26161
hematopoietic cell9.60e-25177
hematopoietic lineage restricted progenitor cell1.02e-24120
nongranular leukocyte2.20e-22115
myeloid leukocyte8.64e-1972
classical monocyte8.72e-1842
CD14-positive, CD16-negative classical monocyte8.72e-1842
myeloid cell9.74e-18108
common myeloid progenitor9.74e-18108
granulocyte monocyte progenitor cell1.62e-1667
myeloid lineage restricted progenitor cell2.86e-1666
defensive cell2.22e-1548
phagocyte2.22e-1548
macrophage dendritic cell progenitor2.30e-1461
monopoietic cell5.31e-1459
monocyte5.31e-1459
monoblast5.31e-1459
promonocyte5.31e-1459
nucleate cell1.20e-0855
lymphoid lineage restricted progenitor cell1.41e-0852
lymphocyte2.83e-0853
common lymphoid progenitor2.83e-0853
mature alpha-beta T cell4.03e-0718
alpha-beta T cell4.03e-0718
immature T cell4.03e-0718
mature T cell4.03e-0718
immature alpha-beta T cell4.03e-0718
Uber Anatomy
Ontology termp-valuen
adult organism6.93e-30114
hematopoietic system4.61e-1998
blood island4.61e-1998
neural tube2.54e-1756
neural rod2.54e-1756
future spinal cord2.54e-1756
neural keel2.54e-1756
hemolymphoid system5.60e-17108
regional part of nervous system6.31e-1653
regional part of brain6.31e-1653
regional part of forebrain1.43e-1541
forebrain1.43e-1541
anterior neural tube1.43e-1541
future forebrain1.43e-1541
central nervous system3.33e-1481
nervous system8.30e-1489
brain1.67e-1368
future brain1.67e-1368
bone marrow6.17e-1376
immune system1.30e-1293
bone element1.56e-1282
telencephalon3.53e-1234
brain grey matter4.95e-1234
gray matter4.95e-1234
regional part of telencephalon1.49e-1132
cerebral hemisphere3.80e-1132
skeletal element1.17e-0990
neurectoderm2.84e-0986
neural plate4.49e-0982
presumptive neural plate4.49e-0982
regional part of cerebral cortex5.86e-0922
cerebral cortex1.62e-0825
pallium1.62e-0825
skeletal system2.29e-08100
neocortex4.44e-0820
pre-chordal neural plate2.33e-0761


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)
MA0003.10.576745
MA0004.10.455723
MA0006.10.812175
MA0007.10.437331
MA0009.10.918715
MA0014.10.134069
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.11.92084
MA0031.11.78748
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.835832
MA0056.10
MA0057.10.0912556
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.11.93074
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.11.05311
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.11.6523
MA0089.10
MA0090.10.391903
MA0091.11.16006
MA0092.10.421159
MA0093.10.818737
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.825856
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.470675
MA0140.10.516266
MA0141.10.944441
MA0142.10.724856
MA0143.10.615094
MA0144.11.17059
MA0145.10.0613434
MA0146.10.65158
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.21.50503
MA0035.20.515566
MA0039.20.881644
MA0138.20.653421
MA0002.20.179788
MA0137.21.55178
MA0104.20.189646
MA0047.20.586412
MA0112.20.208783
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.197713
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.378102
MA0163.10.0517199
MA0164.10.627336
MA0080.20.303167
MA0018.21.46097
MA0099.20.523145
MA0079.20.609448
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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#46738.423690447253280.004171166389609930.01987102342583
CEBPB#105143.985573812912410.01139163688734390.0417420238887554
CHD2#110645.172011417058430.004437884607941780.0210036810879971
E2F1#186974.293965563019419.58670853279727e-050.00137022889346765
ETS1#211344.864380461101170.0055537915159820.0251357441557308
GATA1#262346.780154071900220.001624307209847380.0101678866392502
GTF2F1#296246.369830438378830.002051908375195520.0119108080700892
HEY1#2346284.040111043105711.4081650274634e-050.00033894295299205
HSF1#3297241.07266666666670.001011544990848920.00717890373058377
IRF1#365943.818581876781950.01326136316826170.0469031632608651
MYC#460963.916711403707050.0009649270569246440.00693858557547183
NFKB1#479074.802055496169614.48248622098168e-050.000793737501582071
NRF1#489946.105139723855450.002403740277772550.0135553040426721
POLR2A#543082.147453176558070.002210725788971910.012716086945775
POU2F2#545277.967858550524711.39153702916505e-065.41269034595787e-05
SETDB1#9869315.12000981675390.0007775105067880260.00609216143885022
SIN3A#2594285.408884726815141.36410592556506e-065.3498257138599e-05
SIX5#14791248.54335767772950.000677999305962630.00546918741912652
SPI1#668855.12770219282670.001093354434280730.0076431622330552
TAF1#687283.343046285745296.40776711117462e-050.00104321245412933
TBP#690883.706770687096392.80450451364125e-050.000591955632377078
TFAP2A#702036.194487889891860.009861483862380290.0370476083850048
USF1#739153.975937048254970.003533542098249390.0179380548874286
YY1#752874.297274406122129.53674534900876e-050.0013642078448228
ZNF143#770246.750438276113950.001651292189149780.0103256678806499



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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