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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 11:23, 17 September 2013


Full id: C443_CD4_CD8_Natural_Eosinophils_Neutrophils_Peripheral_blood



Phase1 CAGE Peaks

Hg19::chr11:117103208..117103288,-p2@PCSK7
Hg19::chr12:46123273..46123329,+p3@ARID2
Hg19::chr14:91884150..91884234,-p1@CCDC88C
Hg19::chr15:34394292..34394326,+p1@PGBD4
Hg19::chr17:38297024..38297041,-p@chr17:38297024..38297041
-
Hg19::chr1:100818009..100818072,+p1@CDC14A
Hg19::chr1:155533011..155533044,+p1@LOC645676
Hg19::chr1:226926972..226927038,-p1@ITPKB
Hg19::chr1:231473640..231473651,-p3@EXOC8
Hg19::chr2:234160287..234160335,+p1@ATG16L1
Hg19::chr4:54930662..54930701,-p3@CHIC2
Hg19::chr4:78741344..78741385,-p@chr4:78741344..78741385
-
Hg19::chr4:83351124..83351222,-p4@HNRPDL
Hg19::chr6:12009042..12009092,+p6@HIVEP1
Hg19::chr6:38607628..38607651,-p3@BTBD9
Hg19::chr7:130791091..130791104,+p@chr7:130791091..130791104
+
Hg19::chr7:35734730..35734777,-p1@HERPUD2
Hg19::chr7:39989788..39989876,+p1@CDK13
Hg19::chr8:29940544..29940555,-p3@TMEM66
Hg19::chr8:29940569..29940596,-p1@TMEM66
Hg19::chr8:41909898..41909910,-p4@KAT6A
Hg19::chr8:41909982..41910009,-p2@KAT6A


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
hematopoietic stem cell9.42e-49168
angioblastic mesenchymal cell9.42e-49168
leukocyte2.07e-48136
hematopoietic cell4.80e-45177
hematopoietic oligopotent progenitor cell1.38e-44161
hematopoietic multipotent progenitor cell1.38e-44161
hematopoietic lineage restricted progenitor cell2.56e-39120
nongranular leukocyte4.64e-38115
myeloid cell7.34e-24108
common myeloid progenitor7.34e-24108
myeloid leukocyte4.31e-2372
granulocyte monocyte progenitor cell6.81e-2067
lymphoid lineage restricted progenitor cell1.93e-1952
lymphocyte2.77e-1953
common lymphoid progenitor2.77e-1953
nucleate cell4.40e-1955
classical monocyte7.80e-1942
CD14-positive, CD16-negative classical monocyte7.80e-1942
myeloid lineage restricted progenitor cell1.77e-1866
macrophage dendritic cell progenitor2.01e-1761
defensive cell2.97e-1748
phagocyte2.97e-1748
monopoietic cell1.28e-1659
monocyte1.28e-1659
monoblast1.28e-1659
promonocyte1.28e-1659
mature alpha-beta T cell3.25e-1218
alpha-beta T cell3.25e-1218
immature T cell3.25e-1218
mature T cell3.25e-1218
immature alpha-beta T cell3.25e-1218
T cell4.37e-1225
pro-T cell4.37e-1225
CD8-positive, alpha-beta T cell3.81e-0811
B cell2.37e-0714
lymphocyte of B lineage4.13e-0724
pro-B cell4.13e-0724
Uber Anatomy
Ontology termp-valuen
adult organism2.50e-24114
hematopoietic system4.07e-2398
blood island4.07e-2398
hemolymphoid system3.56e-22108
immune system4.97e-1693
bone marrow2.12e-1476
bone element1.37e-1382
skeletal element1.83e-0990
neural tube2.60e-0956
neural rod2.60e-0956
future spinal cord2.60e-0956
neural keel2.60e-0956
regional part of nervous system1.16e-0853
regional part of brain1.16e-0853
regional part of forebrain1.68e-0841
forebrain1.68e-0841
anterior neural tube1.68e-0841
future forebrain1.68e-0841
blood5.45e-0815
haemolymphatic fluid5.45e-0815
organism substance5.45e-0815
skeletal system3.47e-07100
telencephalon3.49e-0734
brain grey matter4.81e-0734
gray matter4.81e-0734
regional part of telencephalon9.85e-0732


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)
MA0003.19.03163
MA0004.10.478761
MA0006.11.34653
MA0007.10.449227
MA0009.10.526253
MA0014.19.76887
MA0017.10.297619
MA0019.10.262545
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.12.56779
MA0029.10.450974
MA0030.10.441064
MA0031.11.00334
MA0038.10.22896
MA0040.10.456051
MA0041.10.170492
MA0042.10.149889
MA0043.10.526535
MA0046.10.516541
MA0048.11.0794
MA0050.10.150446
MA0051.10.22589
MA0052.10.459414
MA0055.10.631633
MA0056.10
MA0057.10.0785329
MA0058.10.101748
MA0059.10.101051
MA0060.10.0258987
MA0061.10.675348
MA0063.10
MA0066.10.22927
MA0067.10.820123
MA0068.10.514926
MA0069.10.51311
MA0070.10.503171
MA0071.10.201311
MA0072.10.499187
MA0073.13.80114
MA0074.10.639966
MA0076.11.18848
MA0077.10.49237
MA0078.10.30111
MA0081.10.331815
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.11.41674
MA0089.10
MA0090.10.118716
MA0091.10.160096
MA0092.10.4236
MA0093.10.248476
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.538883
MA0103.10.0653004
MA0105.10.447321
MA0106.10.719625
MA0107.10.162095
MA0108.20.383574
MA0109.10
MA0111.10.126618
MA0113.10.272101
MA0114.11.00251
MA0115.10.747865
MA0116.10.377517
MA0117.10.560027
MA0119.10.0925355
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.846727
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.10.660517
MA0139.11.69892
MA0140.10.199454
MA0141.10.100114
MA0142.10.359701
MA0143.10.272236
MA0144.10.0352516
MA0145.10.48721
MA0146.12.58143
MA0147.11.50005
MA0148.10.518828
MA0149.14.01121
MA0062.25.12785
MA0035.20.198962
MA0039.26.54681
MA0138.20.302079
MA0002.20.0227565
MA0137.20.0801516
MA0104.20.792272
MA0047.20.250458
MA0112.20.289137
MA0065.21.9586
MA0150.10.115337
MA0151.10
MA0152.10.20405
MA0153.10.615584
MA0154.10.26587
MA0155.11.40194
MA0156.10.277694
MA0157.10.89541
MA0158.10
MA0159.10.386598
MA0160.10.18494
MA0161.10
MA0162.15.47861
MA0163.13.35831
MA0164.10.28168
MA0080.20.0709213
MA0018.20.722038
MA0099.20.204301
MA0079.215.8252
MA0102.21.03595
MA0258.10.032189
MA0259.10.403807
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#905144.032128276248955.3255677989785e-072.48080720498446e-05
CHD2#110683.761462848769770.0007002358370560630.00563073071961027
CTCF#10664102.436480169579560.003638785887981990.0183936479045037
CTCFL#14069065.38540209790210.0006213706856700010.00511631449390486
E2F1#1869173.792073484224931.62782457128445e-081.18307843006526e-06
E2F6#1876143.192735465625619.67498624322738e-060.000254008518918156
EGR1#1958163.627766614407371.4495292347058e-078.17426478096324e-06
ELF1#1997173.290348422714921.51205004624337e-078.49472806775748e-06
EP300#203382.463251536808440.01035214973756950.0384415348068273
ESR1#209945.594291508391720.005100083402562160.0237196121517719
ETS1#2113125.306596866655823.3208296738816e-071.65944559957187e-05
FOXA1#316963.022205386196030.01131979263328250.0415239304143651
GABPB1#2553134.176358630471281.27824244751352e-065.11096336048486e-05
GTF2B#295968.711953618452064.54391450162014e-050.000799060257004051
GTF2F1#296274.053528460786530.001086335381078520.00759663748673984
HEY1#23462203.672828221005191.00244780445966e-101.08604404823613e-08
HMGN3#9324114.08927386167531.75075923090601e-050.000400016502552161
HNF4A#317244.205870975082490.01366811432388140.0482193011711881
HSF1#3297214.93551515151520.007887097992253930.0323789554722095
IRF1#3659113.818581876781953.37303442817872e-050.000669472334938345
MAX#414982.346383821457140.01378982480437180.0485093978491625
MYC#4609102.373764487095180.004433727172616130.0209887604106996
NFKB1#4790153.741861425586713.73038743635991e-071.83253966823138e-05
NRF1#489984.440101617349420.0002260202218294570.00249448652093909
PAX5#5079123.637944835187911.89263444381865e-050.000428774075223374
POLR2A#5430222.147453176558074.97800844931664e-083.19151764541547e-06
POU2F2#545293.725232569076490.0003013583254279080.00311065053858127
REST#5978104.38637668914912.82986167844788e-050.00059682537123469
SIN3A#25942184.425451140121482.15116950284204e-102.21345804637754e-08
SMC3#912653.419302919302920.01314679266670590.0466147641934509
SP1#6667102.590173353700410.002272441397234830.0129026588608138
TAF1#6872213.191089636393231.5427848500858e-101.63083913925214e-08
TAF7#687984.15747978360870.0003553555440743310.00355795011672698
TBP#6908162.695833226979191.01813841677941e-050.000266700170830261
TCF12#693883.867078146249610.0005812033956957090.00487591786031522
TCF7L2#693462.937320880855640.01293511757195360.0464988381267775
TFAP2A#702086.006776135652712.66432781136025e-050.00057114066562121
YY1#7528153.348525511263991.66506439304847e-066.30520885226935e-05
ZBTB33#1000957.19652841590480.0005265454341736820.00455910119380411
ZBTB7A#51341103.341776958125410.000290672692040720.00308700074069969
ZNF263#1012793.363480669686190.0006495303045566220.00532132848114128



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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