Coexpression cluster:C290: Difference between revisions

Revision as of 14:33, 19 October 2012

Full id: C290_Eosinophils_CD14_Basophils_Mast_CD4_CD8_immature

Phase1 CAGE Peaks

Hg19::chr10:104155305..104155351,-	p@chr10:104155305..104155351 -
Hg19::chr10:27444072..27444081,-	p9@YME1L1
Hg19::chr10:27444113..27444140,-	p3@YME1L1
Hg19::chr11:35068956..35068967,-	p@chr11:35068956..35068967 -
Hg19::chr11:35068999..35069019,-	p@chr11:35068999..35069019 -
Hg19::chr11:35104126..35104150,-	p@chr11:35104126..35104150 -
Hg19::chr12:31945225..31945237,-	p1@H3F3C
Hg19::chr12:62996849..62996863,+	p@chr12:62996849..62996863 +
Hg19::chr14:103243813..103243954,+	p1@TRAF3
Hg19::chr14:24711615..24711644,+	p@chr14:24711615..24711644 +
Hg19::chr14:24711941..24711990,+	p@chr14:24711941..24711990 +
Hg19::chr14:35344580..35344591,-	p3@BAZ1A
Hg19::chr15:45003493..45003500,-	p5@PATL2
Hg19::chr15:66084428..66084478,-	p1@DENND4A
Hg19::chr17:39845134..39845142,+	p1@EIF1
Hg19::chr17:56415424..56415454,-	p@chr17:56415424..56415454 -
Hg19::chr17:63053123..63053164,+	p@chr17:63053123..63053164 +
Hg19::chr17:73775848..73775868,-	p1@H3F3A p1@H3F3B
Hg19::chr18:11851403..11851428,+	p1@CHMP1B
Hg19::chr18:48405312..48405340,-	p@chr18:48405312..48405340 -
Hg19::chr19:47616682..47616696,+	p@chr19:47616682..47616696 +
Hg19::chr19:48825442..48825465,+	p@chr19:48825442..48825465 +
Hg19::chr1:181057828..181057846,+	p1@IER5
Hg19::chr1:203274370..203274382,-	p3@ENST00000432511
Hg19::chr1:204380531..204380560,+	p1@BC009873
Hg19::chr1:45275366..45275381,-	p@chr1:45275366..45275381 -
Hg19::chr1:46153015..46153034,+	p2@TMEM69
Hg19::chr1:66801861..66801890,-	p@chr1:66801861..66801890 -
Hg19::chr20:44600810..44600853,-	p1@ZNF335
Hg19::chr2:128145779..128145837,+	p@chr2:128145779..128145837 +
Hg19::chr3:195269598..195269612,+	p@chr3:195269598..195269612 +
Hg19::chr4:80993447..80993469,+	p@chr4:80993447..80993469 +
Hg19::chr5:40680009..40680062,+	p1@PTGER4
Hg19::chr6:138188378..138188415,+	p1@TNFAIP3
Hg19::chr6:143267648..143267661,-	p@chr6:143267648..143267661 -
Hg19::chr6:16760246..16760257,+	p@chr6:16760246..16760257 +
Hg19::chr6:31240053..31240069,+	p@chr6:31240053..31240069 +
Hg19::chr6:43192145..43192186,-	p@chr6:43192145..43192186 -
Hg19::chr7:115851107..115851141,-	p2@uc003vhn.1
Hg19::chr8:101962922..101962946,+	p@chr8:101962922..101962946 +
Hg19::chr8:123793988..123794016,+	p1@ZHX2
Hg19::chr9:3526360..3526421,-	p5@RFX3
Hg19::chr9:91925676..91925735,-	p@chr9:91925676..91925735 -
Hg19::chr9:96329032..96329074,+	p@chr9:96329032..96329074 +

Enriched pathways on this co-expression clusterSummary: 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. Analyst: Emmanuel Dimont link to source dataset data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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. Analyst: Erik Arner link to source dataset data

GO ID	GO name	FDR corrected p-value
GO:0050789	regulation of biological process	0.0148046825618672
GO:0065007	biological regulation	0.0157128152988876
GO:0050794	regulation of cellular process	0.0247774628528408
GO:0000228	nuclear chromosome	0.0273609379661523
GO:0044424	intracellular part	0.0273609379661523
GO:0003677	DNA binding	0.0273609379661523
GO:0001740	Barr body	0.0273609379661523
GO:0000805	X chromosome	0.0273609379661523
GO:0043231	intracellular membrane-bound organelle	0.0273609379661523
GO:0043227	membrane-bound organelle	0.0273609379661523
GO:0010468	regulation of gene expression	0.0292000980264414
GO:0000803	sex chromosome	0.0292000980264414
GO:0001739	sex chromatin	0.0292000980264414
GO:0031323	regulation of cellular metabolic process	0.0292000980264414
GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB cascade	0.0313510836916462
GO:0019222	regulation of metabolic process	0.0322328454910958
GO:0008270	zinc ion binding	0.0322328454910958
GO:0005634	nucleus	0.0388675441935308
GO:0043283	biopolymer metabolic process	0.0388675441935308
GO:0005720	nuclear heterochromatin	0.0452201402484462
GO:0003676	nucleic acid binding	0.0452201402484462
GO:0016481	negative regulation of transcription	0.0452201402484462
GO:0043229	intracellular organelle	0.0452201402484462
GO:0043226	organelle	0.0452201402484462
GO:0006355	regulation of transcription, DNA-dependent	0.0452201402484462
GO:0046914	transition metal ion binding	0.0452201402484462
GO:0044464	cell part	0.0452201402484462
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0452201402484462
GO:0004957	prostaglandin E receptor activity	0.0452201402484462
GO:0006351	transcription, DNA-dependent	0.0452201402484462
GO:0032774	RNA biosynthetic process	0.0452201402484462
GO:0030278	regulation of ossification	0.0455985375246441
GO:0005622	intracellular	0.0455985375246441
GO:0000792	heterochromatin	0.0459337836461696
GO:0048523	negative regulation of cellular process	0.0459337836461696
GO:0004955	prostaglandin receptor activity	0.0459337836461696
GO:0000790	nuclear chromatin	0.0459337836461696
GO:0045449	regulation of transcription	0.0459337836461696
GO:0031324	negative regulation of cellular metabolic process	0.0459337836461696
GO:0046850	regulation of bone remodeling	0.0459337836461696
GO:0048519	negative regulation of biological process	0.0459337836461696
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0459337836461696
GO:0004953	icosanoid receptor activity	0.0459337836461696
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0459337836461696
GO:0004954	prostanoid receptor activity	0.0459337836461696
GO:0006350	transcription	0.0459337836461696
GO:0010467	gene expression	0.0459337836461696
GO:0006402	mRNA catabolic process	0.0471613307300842
GO:0009892	negative regulation of metabolic process	0.0488373563300737

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji links to source dataset cell_data uberon_data

Cell Type
Ontology term	p-value	n
leukocyte	8.31e-87	136
hematopoietic stem cell	4.66e-72	168
angioblastic mesenchymal cell	4.66e-72	168
hematopoietic cell	2.22e-69	177
hematopoietic lineage restricted progenitor cell	2.71e-68	120
nongranular leukocyte	3.18e-67	115
hematopoietic oligopotent progenitor cell	6.85e-66	161
hematopoietic multipotent progenitor cell	6.85e-66	161
classical monocyte	3.23e-43	42
CD14-positive, CD16-negative classical monocyte	3.23e-43	42
myeloid leukocyte	4.76e-41	72
defensive cell	4.78e-36	48
phagocyte	4.78e-36	48
granulocyte monocyte progenitor cell	7.42e-36	67
lymphocyte	1.48e-32	53
common lymphoid progenitor	1.48e-32	53
lymphoid lineage restricted progenitor cell	3.55e-32	52
myeloid lineage restricted progenitor cell	6.64e-32	66
macrophage dendritic cell progenitor	1.84e-31	61
myeloid cell	2.16e-31	108
common myeloid progenitor	2.16e-31	108
nucleate cell	7.25e-31	55
monopoietic cell	9.19e-30	59
monocyte	9.19e-30	59
monoblast	9.19e-30	59
promonocyte	9.19e-30	59
mesenchymal cell	7.69e-19	354
connective tissue cell	6.80e-18	361
T cell	2.25e-16	25
pro-T cell	2.25e-16	25
mature alpha-beta T cell	4.03e-16	18
alpha-beta T cell	4.03e-16	18
immature T cell	4.03e-16	18
mature T cell	4.03e-16	18
immature alpha-beta T cell	4.03e-16	18
lymphocyte of B lineage	7.21e-14	24
pro-B cell	7.21e-14	24
motile cell	1.85e-13	386
stuff accumulating cell	1.16e-12	87
multi fate stem cell	9.00e-12	427
stem cell	1.68e-11	441
somatic stem cell	3.23e-11	433
B cell	5.56e-10	14
CD8-positive, alpha-beta T cell	7.24e-10	11
intermediate monocyte	1.52e-09	9
CD14-positive, CD16-positive monocyte	1.52e-09	9
granulocyte	2.72e-09	8
blood cell	7.89e-08	11
CD4-positive, alpha-beta T cell	1.83e-07	6

Uber Anatomy
Ontology term	p-value	n
hematopoietic system	4.85e-46	98
blood island	4.85e-46	98
hemolymphoid system	5.44e-43	108
immune system	1.14e-33	93
bone marrow	2.49e-32	76
bone element	8.93e-29	82
skeletal element	8.52e-25	90
skeletal system	1.51e-21	100
connective tissue	1.31e-16	371
lateral plate mesoderm	2.10e-13	203
blood	4.19e-10	15
haemolymphatic fluid	4.19e-10	15
organism substance	4.19e-10	15
musculoskeletal system	1.05e-07	167

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon link to source data Novel motifs data Jaspar motifs data

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysisSummary: 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. Analyst: Erik Arner link to source dataset data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ATF3#467	7	3.57368685641048	0.00310654674088054	0.0163332981811731
BCL3#602	12	9.42193712829227	3.0434066534761e-09	2.54687778431403e-07
BCLAF1#9774	10	4.92105627502769	2.56364832317549e-05	0.000554566833521385
BRCA1#672	7	3.21112760233105	0.00557231244400177	0.0252151966784706
CCNT2#905	22	3.16810078848132	1.33016809544966e-07	7.57891029572651e-06
CHD2#1106	12	2.82109713657732	0.000727717950822339	0.00580390493057918
CTCF#10664	15	1.82736012718467	0.0109759030841821	0.040380172685955
E2F1#1869	27	3.01135247276686	3.72381991061812e-09	3.05748449406483e-07
E2F4#1874	14	4.03074646395414	4.26193893615668e-06	0.000135005350486281
E2F6#1876	24	2.73663039910766	3.95038382298945e-07	1.91538596141687e-05
EBF1#1879	15	3.0362955158758	5.30616995055974e-05	0.000900066726435779
EGR1#1958	31	3.51439890770714	7.2196106577002e-13	1.03857977614263e-10
ELF1#1997	33	3.19357346910565	7.6460260582827e-13	1.09539549451439e-10
ELK4#2005	9	3.32093488468664	0.00125517246421214	0.00843558281787977
EP300#2033	16	2.46325153680844	0.000333918590381299	0.00340003155511675
ETS1#2113	13	2.87440663610524	0.000340557694941781	0.00346122081568944
FOS#2353	13	2.65848679580971	0.00072436434752468	0.0057789235422145
FOSL2#2355	10	3.84777286467311	0.000199143169088824	0.00239116043187718
GABPB1#2553	18	2.89132520571089	1.28776074496936e-05	0.000315709963483227
GATA1#2623	13	4.00645467885013	1.11010742851811e-05	0.000284441878623657
GTF2B#2959	10	7.25996134871005	8.38897660627985e-07	3.65056803243026e-05
GTF2F1#2962	13	3.76399071358749	2.16259023031474e-05	0.000476193887969304
HEY1#23462	32	2.93826257680415	3.08465847714837e-11	3.55976405187733e-09
HMGN3#9324	24	4.4610260309185	1.80238990752895e-11	2.17870138370851e-09
IRF1#3659	20	3.47143806980177	1.59551320186378e-07	8.84937882578073e-06
IRF3#3661	4	4.27108656468087	0.0141488487286433	0.0496436072153052
IRF4#3662	8	3.9844568521353	0.000760434436547546	0.00597225237769507
JUN#3725	9	2.55944233479607	0.00719786055949144	0.029819014635967
JUND#3727	18	2.86145343076542	1.48954987896922e-05	0.000353080117588892
MAX#4149	17	2.49303281029821	0.000170021355720951	0.00207682577428542
MEF2A#4205	7	2.9818776447161	0.00826071535355566	0.0325501169896246
MEF2C#4208	8	7.51115536229528	9.53985594576662e-06	0.000253390899064069
MXI1#4601	11	2.49039290718982	0.00345224390681974	0.0175483744468192
MYC#4609	23	2.72982916015946	8.93997301163262e-07	3.85182277789563e-05
NANOG#79923	6	3.98792433831991	0.00369096212586596	0.0186231408987543
NFKB1#4790	29	3.61713271140048	4.52174270108211e-12	5.94020485482156e-10
NFYA#4800	9	3.76886877951079	0.000509579998013114	0.0044643927030024
NFYB#4801	11	4.18994831338411	4.13201003684635e-05	0.000750248602639423
NR2C2#7182	5	3.70620578468646	0.0108819740346939	0.0401264868202307
NRF1#4899	12	3.33007621301206	0.000158276523829502	0.00199496039973803
PAX5#5079	29	4.39585000918539	2.75268485180949e-14	4.58513003569588e-12
POLR2A#5430	41	2.00103591452002	5.27129681590154e-11	5.91966632425743e-09
POU2F2#5452	27	5.58784885361473	1.2692889424603e-15	2.36298160181125e-13
RDBP#7936	5	17.458909544321	1.01923052103961e-05	0.000266384925893032
REST#5978	13	2.85114484794692	0.000368753291961277	0.00367132746035689
RFX5#5993	15	4.10724232745287	1.35237203105121e-06	5.31978841999839e-05
RXRA#6256	8	3.64993038893332	0.00133826253230811	0.00887239259897963
SIN3A#25942	27	3.31908835509111	3.92732006451198e-10	3.8804671732977e-08
SMARCB1#6598	11	4.56317894528935	1.8836493517578e-05	0.000427480344737576
SMC3#9126	8	2.73544233544234	0.00779800849946887	0.0320333625580565
SP1#6667	24	3.10820802444049	3.22972172072396e-08	2.17338213138331e-06
SPI1#6688	17	3.16985226465651	7.43411407159201e-06	0.000212948831465441
SREBF1#6720	4	4.27325904004439	0.0141249101522424	0.0495646101330526
STAT3#6774	10	2.39078749935324	0.00725571167066672	0.0300277092713886
TAF1#6872	38	2.88717633768912	1.07374624158114e-14	1.85356997891723e-12
TAF7#6879	16	4.1574797836087	4.44122303686873e-07	2.11507931029427e-05
TBP#6908	36	3.03281238035159	5.06581319072389e-14	8.22812540942476e-12
TCF12#6938	18	4.35046291453081	3.01792345088513e-08	2.0466812161493e-06
TCF7L2#6934	11	2.69254414078434	0.00186478526581827	0.0109994526362134
TFAP2A#7020	11	4.12965859326124	4.71529045360775e-05	0.000824477180117763
TFAP2C#7022	18	4.42195715857918	2.34378191509229e-08	1.64947600694288e-06
USF1#7391	16	2.31327246443926	0.00068439095124238	0.00551946768778401
USF2#7392	14	4.13388098615851	3.17273019452934e-06	0.000106889280253693
YY1#7528	31	3.46014302830613	1.11370161383446e-12	1.55916733039219e-10
ZEB1#6935	8	3.07062400318979	0.00392316266644974	0.019115945960686
ZNF263#10127	16	2.98976059527661	3.24708036830591e-05	0.000646315659587385

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. Analyst:NA link to data source data

@@ Line 5: / Line 5: @@
 |id=C290
 |kegg_enrichment=hsa05322;Systemic_lupus_erythematosus;9.10E-06
-|ontology_enrichment_celltype=CL:0000738!8.88e-56!140;CL:0000037!5.33e-47!172;CL:0000566!5.33e-47!172;CL:0002031!4.30e-45!124;CL:0000988!5.87e-45!182;CL:0002087!7.53e-44!119;CL:0002032!3.05e-43!165;CL:0000837!3.05e-43!165;CL:0000766!7.23e-27!76;CL:0002057!3.57e-26!42;CL:0000557!9.32e-24!71;CL:0000860!1.49e-23!45;CL:0000839!9.14e-22!70;CL:0000542!2.40e-21!53;CL:0000051!2.40e-21!53;CL:0000838!3.23e-21!52;CL:0000763!3.32e-21!112;CL:0000049!3.32e-21!112;CL:0002009!4.73e-21!65;CL:0002194!5.08e-20!63;CL:0000576!5.08e-20!63;CL:0000040!5.08e-20!63;CL:0000559!5.08e-20!63;CL:0000084!7.93e-11!25;CL:0000827!7.93e-11!25;CL:0000791!3.43e-10!18;CL:0000789!3.43e-10!18;CL:0002420!3.43e-10!18;CL:0002419!3.43e-10!18;CL:0000790!3.43e-10!18;CL:0000945!8.23e-10!24;CL:0000826!8.23e-10!24;CL:0000134!1.66e-08!358;CL:0002320!3.65e-08!365;CL:0000236!4.92e-07!14
+|ontology_enrichment_celltype=CL:0000738!8.31e-87!136;CL:0000037!4.66e-72!168;CL:0000566!4.66e-72!168;CL:0000988!2.22e-69!177;CL:0002031!2.71e-68!120;CL:0002087!3.18e-67!115;CL:0002032!6.85e-66!161;CL:0000837!6.85e-66!161;CL:0000860!3.23e-43!42;CL:0002057!3.23e-43!42;CL:0000766!4.76e-41!72;CL:0000473!4.78e-36!48;CL:0000234!4.78e-36!48;CL:0000557!7.42e-36!67;CL:0000542!1.48e-32!53;CL:0000051!1.48e-32!53;CL:0000838!3.55e-32!52;CL:0000839!6.64e-32!66;CL:0002009!1.84e-31!61;CL:0000763!2.16e-31!108;CL:0000049!2.16e-31!108;CL:0002242!7.25e-31!55;CL:0002194!9.19e-30!59;CL:0000576!9.19e-30!59;CL:0000040!9.19e-30!59;CL:0000559!9.19e-30!59;CL:0000134!7.69e-19!354;CL:0002320!6.80e-18!361;CL:0000084!2.25e-16!25;CL:0000827!2.25e-16!25;CL:0000791!4.03e-16!18;CL:0000789!4.03e-16!18;CL:0002420!4.03e-16!18;CL:0002419!4.03e-16!18;CL:0000790!4.03e-16!18;CL:0000945!7.21e-14!24;CL:0000826!7.21e-14!24;CL:0000219!1.85e-13!386;CL:0000325!1.16e-12!87;CL:0000048!9.00e-12!427;CL:0000034!1.68e-11!441;CL:0000723!3.23e-11!433;CL:0000236!5.56e-10!14;CL:0000625!7.24e-10!11;CL:0002393!1.52e-09!9;CL:0002397!1.52e-09!9;CL:0000094!2.72e-09!8;CL:0000081!7.89e-08!11;CL:0000624!1.83e-07!6
 |ontology_enrichment_disease=
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 }}

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Coexpression cluster:C290: Difference between revisions

From FANTOM5_SSTAR

Revision as of 14:33, 19 October 2012

Phase1 CAGE Peaks

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