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Coexpression cluster:C509: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C509_Neutrophils_Eosinophils_CD14_Whole_CD34_CD19_Peripheral
|full_id=C509_Neutrophils_Eosinophils_CD14_Whole_CD34_CD19_Peripheral
|gostat_on_coexpression_clusters=GO:0030133!transport vesicle!0.0188889352968199!79666;54812$GO:0007254!JNK cascade!0.0188889352968199!51347;10746$GO:0031098!stress-activated protein kinase signaling pathway!0.0188889352968199!51347;10746$GO:0007243!protein kinase cascade!0.0188889352968199!3454;51347;10746$GO:0043687!post-translational protein modification!0.0277494551879854!81545;1540;8897;51347;10746$GO:0019962!interferon-alpha/beta binding!0.0277494551879854!3454$GO:0004905!interferon-alpha/beta receptor activity!0.0277494551879854!3454$GO:0046329!negative regulation of JNK cascade!0.0322552606000145!51347$GO:0005737!cytoplasm!0.0322552606000145!81545;1540;8897;50618;79666;51347;10746;54812$GO:0000165!MAPKKK cascade!0.0322552606000145!51347;10746$GO:0006464!protein modification process!0.0322552606000145!81545;1540;8897;51347;10746$GO:0030121!AP-1 adaptor complex!0.0322552606000145!54812$GO:0019961!interferon binding!0.0322552606000145!3454$GO:0004904!interferon receptor activity!0.0322552606000145!3454$GO:0044424!intracellular part!0.0322552606000145!81545;50618;79666;51347;1655;1540;8897;26959;54812;10746$GO:0043412!biopolymer modification!0.0322552606000145!81545;1540;8897;51347;10746$GO:0045786!negative regulation of progression through cell cycle!0.0408542297560198!1540;26959$GO:0045351!interferon type I biosynthetic process!0.0408542297560198!3454$GO:0032606!interferon type I production!0.0408542297560198!3454
|gostat_on_coexpression_clusters=GO:0030133!transport vesicle!0.0188889352968199!79666;54812$GO:0007254!JNK cascade!0.0188889352968199!51347;10746$GO:0031098!stress-activated protein kinase signaling pathway!0.0188889352968199!51347;10746$GO:0007243!protein kinase cascade!0.0188889352968199!3454;51347;10746$GO:0043687!post-translational protein modification!0.0277494551879854!81545;1540;8897;51347;10746$GO:0019962!interferon-alpha/beta binding!0.0277494551879854!3454$GO:0004905!interferon-alpha/beta receptor activity!0.0277494551879854!3454$GO:0046329!negative regulation of JNK cascade!0.0322552606000145!51347$GO:0005737!cytoplasm!0.0322552606000145!81545;1540;8897;50618;79666;51347;10746;54812$GO:0000165!MAPKKK cascade!0.0322552606000145!51347;10746$GO:0006464!protein modification process!0.0322552606000145!81545;1540;8897;51347;10746$GO:0030121!AP-1 adaptor complex!0.0322552606000145!54812$GO:0019961!interferon binding!0.0322552606000145!3454$GO:0004904!interferon receptor activity!0.0322552606000145!3454$GO:0044424!intracellular part!0.0322552606000145!81545;50618;79666;51347;1655;1540;8897;26959;54812;10746$GO:0043412!biopolymer modification!0.0322552606000145!81545;1540;8897;51347;10746$GO:0045786!negative regulation of progression through cell cycle!0.0408542297560198!1540;26959$GO:0045351!interferon type I biosynthetic process!0.0408542297560198!3454$GO:0032606!interferon type I production!0.0408542297560198!3454

Revision as of 18:05, 12 September 2012


Full id: C509_Neutrophils_Eosinophils_CD14_Whole_CD34_CD19_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:99894399..99894453,+p1@C10orf28
Hg19::chr11:95522907..95522989,-p1@FAM76B
Hg19::chr12:105501487..105501562,+p1@KIAA1033
Hg19::chr12:118810688..118810744,-p1@TAOK3
Hg19::chr16:50775971..50776014,+p1@CYLD
Hg19::chr17:62502968..62503006,-p2@DDX5
Hg19::chr18:9137005..9137035,+p@chr18:9137005..9137035
+
Hg19::chr21:34697258..34697336,+p1@IFNAR1
Hg19::chr22:30279148..30279192,+p1@MTMR3
Hg19::chr2:128145498..128145563,-p1@MAP3K2
Hg19::chr2:24583314..24583433,-p1@ITSN2
Hg19::chr2:64751475..64751556,+p1@AFTPH
Hg19::chr5:147763539..147763586,+p1@FBXO38
Hg19::chr7:106809432..106809455,+p1@HBP1
Hg19::chr8:96145974..96146041,+p1@PLEKHF2
Hg19::chrX:100663186..100663241,+p1@HNRNPH2
Hg19::chrX:44732415..44732450,+p1@KDM6A
Hg19::chrX:54070731..54070781,-p1@PHF8


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:0030133transport vesicle0.0188889352968199
GO:0007254JNK cascade0.0188889352968199
GO:0031098stress-activated protein kinase signaling pathway0.0188889352968199
GO:0007243protein kinase cascade0.0188889352968199
GO:0043687post-translational protein modification0.0277494551879854
GO:0019962interferon-alpha/beta binding0.0277494551879854
GO:0004905interferon-alpha/beta receptor activity0.0277494551879854
GO:0046329negative regulation of JNK cascade0.0322552606000145
GO:0005737cytoplasm0.0322552606000145
GO:0000165MAPKKK cascade0.0322552606000145
GO:0006464protein modification process0.0322552606000145
GO:0030121AP-1 adaptor complex0.0322552606000145
GO:0019961interferon binding0.0322552606000145
GO:0004904interferon receptor activity0.0322552606000145
GO:0044424intracellular part0.0322552606000145
GO:0043412biopolymer modification0.0322552606000145
GO:0045786negative regulation of progression through cell cycle0.0408542297560198
GO:0045351interferon type I biosynthetic process0.0408542297560198
GO:0032606interferon type I production0.0408542297560198



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
leukocyte1.26e-44140
hematopoietic stem cell3.25e-38172
angioblastic mesenchymal cell3.25e-38172
hematopoietic lineage restricted progenitor cell2.43e-37124
hematopoietic oligopotent progenitor cell1.05e-35165
hematopoietic multipotent progenitor cell1.05e-35165
nongranular leukocyte4.54e-34119
hematopoietic cell2.47e-32182
myeloid leukocyte4.70e-3276
granulocyte monocyte progenitor cell2.21e-2871
myeloid lineage restricted progenitor cell1.35e-2770
CD14-positive, CD16-negative classical monocyte5.65e-2742
myeloid cell8.75e-26112
common myeloid progenitor8.75e-26112
macrophage dendritic cell progenitor1.60e-2565
classical monocyte1.52e-2445
monopoietic cell1.54e-2463
monocyte1.54e-2463
monoblast1.54e-2463
promonocyte1.54e-2463
lymphoid lineage restricted progenitor cell1.52e-0952
lymphocyte4.22e-0953
common lymphoid progenitor4.22e-0953
mature alpha-beta T cell7.08e-0818
alpha-beta T cell7.08e-0818
immature T cell7.08e-0818
mature T cell7.08e-0818
immature alpha-beta T cell7.08e-0818
mesenchymal cell1.06e-07358
connective tissue cell7.34e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.55e-31102
blood island8.55e-31102
hemolymphoid system2.58e-28112
adult organism7.74e-26115
bone marrow5.29e-2480
bone element2.65e-2286
skeletal element4.91e-19101
skeletal system4.91e-19101
immune system1.67e-17115
neural tube2.26e-0857
neural rod2.26e-0857
future spinal cord2.26e-0857
neural keel2.26e-0857
anterior neural tube1.18e-0742
regional part of forebrain1.99e-0741
forebrain1.99e-0741
future forebrain1.99e-0741


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)

{{{tfbs_overrepresentation_jaspar}}}



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#46778.735678982336747.11832414395998e-060.000205197531126425
BHLHE40#855349.971514121550540.0005867890152550460.00491567000595346
BRCA1#67255.606730734228820.00148351682127060.00948903805099707
CCNT2#905144.928156782082059.60784791139458e-097.30833232351157e-07
CHD2#1106116.321347287515861.14456586357404e-076.64096190143384e-06
E2F1#1869143.816858278239472.80080033108096e-071.41927601056654e-05
E2F4#187485.630249029015313.19335818496187e-050.000640997761828238
EBF1#187962.968822282189670.01122401152627930.0412131118304356
EGR1#1958133.602573790696212.58786130943899e-069.08788323122052e-05
ELF1#1997153.548414965672951.40980687262883e-077.9847516252973e-06
ELK4#200576.313876200515345.82725740562361e-050.000969097032143192
EP300#203383.010640767210310.002449702240952020.0137891803569466
ETS1#211394.864380461101172.6061409457402e-050.000562826208089662
FOS#235373.499204842347820.002184794619119820.0126009368912224
FOSL2#235565.643400201520560.0004238997356359670.00396237935112188
FOXA1#316974.30944101364990.0006312507809548920.00518417868303436
GABPB1#255393.533841918091090.0003266634257492130.00333005383326716
GATA1#262364.520102714600150.001371779480240890.009025278892332
GTF2B#295947.098628874294270.002064127539227270.0119710915187337
GTF2F1#296264.246553625585880.001895373487637690.011164744031325
HEY1#23462163.591209816093961.78396865355315e-081.28760125921519e-06
HMGN3#932483.634910099266930.000697360510488150.00560933721155822
HNF4A#317245.140508969545260.006558627673544430.0280325973234011
HNF4G#317457.987061812901890.0002976702118892140.00310604248771082
IRF1#3659166.788590003167918.74521507392966e-131.23759013158013e-10
IRF3#3661410.44043382477550.000493773906886250.00436694496242637
JUN#372553.475785886760090.01153499712370480.0421844514532742
JUND#3727103.885924412150575.14688713080812e-050.000876036090375602
MAX#4149134.660178978727371.17151458807717e-076.76350536562697e-06
MXI1#460194.980785814379652.15158679768434e-050.000473970836455082
MYC#4609123.48152124773961.40881703397654e-050.000338943658630444
NFE2#4778417.15650236702877.43078141794464e-050.00115142934793579
NFKB1#4790164.878278599283411.5468342524303e-101.63181638878352e-08
NFYA#480099.212790349915261.26299161532635e-077.22770308564758e-06
NFYB#480187.448797001571764.07516661513521e-060.000129521097418779
PAX5#5079124.446377020785229.8090335066856e-074.16272104999893e-05
PBX3#509056.08736463520670.00102688891506630.00727543934608296
POLR2A#5430182.147453176558071.059158074972e-064.41234185049864e-05
POU2F2#545284.047166247885570.0003333649302719250.00339472503438666
SIN3A#25942164.807897534946791.94005847662396e-102.01609718646896e-08
SIX5#14791287.594095713537333.52877746851906e-060.000116553444033732
SP1#6667103.16576743230050.0003042284203438780.00313841485502709
SP2#666857.264869581623510.0004602651152282540.00424081414815382
SPI1#668873.190570253314390.003725697551062360.0185749535294731
SREBF1#672037.834308240081380.006180412423529390.0273205829637258
TAF1#6872173.157321492092781.58473138591732e-081.16064348677292e-06
TAF7#687995.716534702461966.97179630487212e-060.000201362675410547
TBP#6908163.294907277419016.69614874550662e-084.07302899727412e-06
TCF12#693863.544821634062140.004732116341051210.0222911685780095
TCF7L2#693474.188401996775630.0007501787427136260.00590591871779499
TFAP2C#702274.203588903834530.0007339404613321410.00584416040264314
USF1#7391155.30124939767334.46175296849933e-104.35089652919796e-08
USF2#739296.49609869253482.41613336419054e-068.55095060734312e-05
YY1#7528143.819799472108552.77275053238948e-071.40642687155039e-05
ZEB1#693554.69123111598440.003248544879166750.0168282713474181
ZNF143#770286.000389578767962.00891846238146e-050.000445833904149294
ZNF263#10127104.567689798339261.21695898680601e-050.000302974921628207



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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