Personal tools

Coexpression cluster:C213: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0319790978673642,0.0182698989373361,0.0329050193664387,0.65708249243269,0.609662182129482,0.628505263455421,0,0,0,0,0,0.111800154394222,0.99404982910804,0.945529315705004,0.93426510552099,0,0,0,0.110857771591861,0.139210117864267,0.0943257785523457,0.229755313179946,0.149578685266771,0.28535904381024,0.270230845683375,0.306348418993444,0.364786628965105,0.486922459690655,0.360019282223445,0.422017155880064,0.194438581726263,0.114376807359093,0.223799672996739,0.537651782554888,0.358642115221847,0.551126413850657,0.123803082231165,0.145795150225341,0.154187968871398,0.462352250106456,0.329351182440039,0.351341005362286,0.243966692437341,0.310261104275252,0.319302691559872,0.295913844697094,0.323217625098021,0.507212952056032,0.153055502916071,0.355035778292347,0.311392129055566,0.193581802139666,0.204311999163507,0.12105112091666,0.108907434678255,0.0787890013723437,0.135237094603344,0,0,0,0,0,0,0,0,0.515456810409039,0.524908502418249,0.466874220417106,0.365808586596611,0.510817598835734,0,0.472331847080797,0.574155786915165,0.58865494810798,0,0.122518063916678,0.168334756349589,0,0.0458744785985099,0.201181785145201,0.159286732874341,0.104078526590485,0.0523442574910016,0.100411454806203,0,0,0,0.112797015870854,0.102961957061387,0,0,0.368412469759673,0.307684762345384,0.245280425003452,0,0,0,0.0609149782727745,0,0,0,0,0.783300787974288,0.82086130648608,0.678102504714794,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.234383601705801,0.196451135708678,0.13718235424895,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.560577092055277,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.351016793561865,0.333035885936016,0.400522309803123,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.875177933188226,0.920714730323758,0.952175580518536,0,0,0,0,0,0.242791553592671,0,0.197396008416614,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.308316812342537,0.626926527118698,0.396928803964221,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.112779598617622,0,0,0,0,0,0,0,0,0,0,0,0.0266094859650764,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.161352362291136,0.406131906607941,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0963667653352072,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0375633914926427,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C213_CD14_Natural_CD8_CD4_Basophils_Eosinophils_Peripheral
|full_id=C213_CD14_Natural_CD8_CD4_Basophils_Eosinophils_Peripheral
|gostat_on_coexpression_clusters=GO:0004337!geranyltranstransferase activity!0.0141261637694952!9453$GO:0004161!dimethylallyltranstransferase activity!0.0141261637694952!9453$GO:0031616!spindle pole centrosome!0.0141261637694952!54820$GO:0031229!intrinsic to nuclear inner membrane!0.0141261637694952!23592$GO:0005639!integral to nuclear inner membrane!0.0141261637694952!23592$GO:0004311!farnesyltranstransferase activity!0.0141261637694952!9453$GO:0051298!centrosome duplication!0.0211845680019452!54820$GO:0007098!centrosome cycle!0.0346376062360266!54820$GO:0005637!nuclear inner membrane!0.0346376062360266!23592$GO:0051297!centrosome organization and biogenesis!0.0346376062360266!54820$GO:0031023!microtubule organizing center organization and biogenesis!0.0346376062360266!54820$GO:0004659!prenyltransferase activity!0.0370348186593884!9453
|gostat_on_coexpression_clusters=GO:0004337!geranyltranstransferase activity!0.0141261637694952!9453$GO:0004161!dimethylallyltranstransferase activity!0.0141261637694952!9453$GO:0031616!spindle pole centrosome!0.0141261637694952!54820$GO:0031229!intrinsic to nuclear inner membrane!0.0141261637694952!23592$GO:0005639!integral to nuclear inner membrane!0.0141261637694952!23592$GO:0004311!farnesyltranstransferase activity!0.0141261637694952!9453$GO:0051298!centrosome duplication!0.0211845680019452!54820$GO:0007098!centrosome cycle!0.0346376062360266!54820$GO:0005637!nuclear inner membrane!0.0346376062360266!23592$GO:0051297!centrosome organization and biogenesis!0.0346376062360266!54820$GO:0031023!microtubule organizing center organization and biogenesis!0.0346376062360266!54820$GO:0004659!prenyltransferase activity!0.0370348186593884!9453

Revision as of 14:49, 12 September 2012


Full id: C213_CD14_Natural_CD8_CD4_Basophils_Eosinophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:102130575..102130607,+p@chr10:102130575..102130607
+
Hg19::chr10:105881496..105881525,-p@chr10:105881496..105881525
-
Hg19::chr10:127730695..127730726,+p@chr10:127730695..127730726
+
Hg19::chr10:17248566..17248644,+p@chr10:17248566..17248644
+
Hg19::chr10:17270419..17270434,-p@chr10:17270419..17270434
-
Hg19::chr10:33269613..33269628,+p@chr10:33269613..33269628
+
Hg19::chr10:33269657..33269672,+p@chr10:33269657..33269672
+
Hg19::chr10:3825708..3825723,+p@chr10:3825708..3825723
+
Hg19::chr10:3826863..3826874,-p@chr10:3826863..3826874
-
Hg19::chr10:3847651..3847673,+p@chr10:3847651..3847673
+
Hg19::chr10:3847675..3847688,+p@chr10:3847675..3847688
+
Hg19::chr10:90753989..90754005,-p@chr10:90753989..90754005
-
Hg19::chr11:102187946..102187979,-p@chr11:102187946..102187979
-
Hg19::chr12:122224417..122224427,+p@chr12:122224417..122224427
+
Hg19::chr12:122228022..122228041,+p@chr12:122228022..122228041
+
Hg19::chr12:65563377..65563392,+p2@LEMD3
Hg19::chr12:76478857..76478871,+p@chr12:76478857..76478871
+
Hg19::chr12:96793473..96793491,+p@chr12:96793473..96793491
+
Hg19::chr13:114896468..114896497,-p@chr13:114896468..114896497
-
Hg19::chr13:47128179..47128209,-p@chr13:47128179..47128209
-
Hg19::chr13:99934915..99934930,-p@chr13:99934915..99934930
-
Hg19::chr14:70233907..70233918,+p2@SRSF5
Hg19::chr14:77422765..77422782,-p@chr14:77422765..77422782
-
Hg19::chr14:93049440..93049476,-p@chr14:93049440..93049476
-
Hg19::chr15:42229070..42229082,+p@chr15:42229070..42229082
+
Hg19::chr16:15737263..15737283,+p2@NDE1
Hg19::chr17:2498730..2498733,+p@chr17:2498730..2498733
+
Hg19::chr17:33570639..33570656,-p@chr17:33570639..33570656
-
Hg19::chr17:7744740..7744755,-p@chr17:7744740..7744755
-
Hg19::chr17:8867066..8867104,-p@chr17:8867066..8867104
-
Hg19::chr18:11851090..11851103,+p5@CHMP1B
Hg19::chr18:57572110..57572120,-p@chr18:57572110..57572120
-
Hg19::chr19:14229527..14229543,-p@chr19:14229527..14229543
-
Hg19::chr19:44099470..44099492,+p@chr19:44099470..44099492
+
Hg19::chr1:15735925..15735938,-p2@ENST00000427824
Hg19::chr1:171453206..171453207,-p@chr1:171453206..171453207
-
Hg19::chr1:2187769..2187789,+p@chr1:2187769..2187789
+
Hg19::chr1:235490525..235490573,+p5@GGPS1
Hg19::chr1:54872206..54872236,+p@chr1:54872206..54872236
+
Hg19::chr1:59250046..59250065,+p@chr1:59250046..59250065
+
Hg19::chr1:59281989..59282008,-p@chr1:59281989..59282008
-
Hg19::chr20:35201225..35201242,-p@chr20:35201225..35201242
-
Hg19::chr20:56881907..56881918,-p@chr20:56881907..56881918
-
Hg19::chr21:43653871..43653885,+p@chr21:43653871..43653885
+
Hg19::chr21:43654826..43654849,-p@chr21:43654826..43654849
-
Hg19::chr2:161263682..161263696,+p@chr2:161263682..161263696
+
Hg19::chr2:178077094..178077105,-p@chr2:178077094..178077105
-
Hg19::chr2:97203110..97203159,+p4@ARID5A
Hg19::chr3:119013380..119013388,-p@chr3:119013380..119013388
-
Hg19::chr3:119013997..119014002,+p@chr3:119013997..119014002
+
Hg19::chr3:5018897..5018920,-p@chr3:5018897..5018920
-
Hg19::chr3:5020060..5020082,-p@chr3:5020060..5020082
-
Hg19::chr3:5020146..5020171,+p@chr3:5020146..5020171
+
Hg19::chr4:103457066..103457069,+p@chr4:103457066..103457069
+
Hg19::chr4:107237802..107237819,+p@chr4:107237802..107237819
+
Hg19::chr4:107237829..107237840,+p@chr4:107237829..107237840
+
Hg19::chr5:100237813..100237824,-p@chr5:100237813..100237824
-
Hg19::chr5:133984176..133984203,-p@chr5:133984176..133984203
-
Hg19::chr6:143265842..143265868,+p@chr6:143265842..143265868
+
Hg19::chr6:150260042..150260087,-p@chr6:150260042..150260087
-
Hg19::chr6:44094627..44094662,+p3@TMEM63B
Hg19::chr7:104585602..104585616,-p@chr7:104585602..104585616
-
Hg19::chr7:104652294..104652297,-p@chr7:104652294..104652297
-
Hg19::chr7:105316500..105316514,+p@chr7:105316500..105316514
+
Hg19::chr7:48128459..48128476,-p@chr7:48128459..48128476
-
Hg19::chr8:141599124..141599145,+p@chr8:141599124..141599145
+
Hg19::chr9:123688609..123688619,+p@chr9:123688609..123688619
+
Hg19::chr9:128000415..128000420,-p@chr9:128000415..128000420
-
Hg19::chr9:5437979..5437984,+p@chr9:5437979..5437984
+


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:0004337geranyltranstransferase activity0.0141261637694952
GO:0004161dimethylallyltranstransferase activity0.0141261637694952
GO:0031616spindle pole centrosome0.0141261637694952
GO:0031229intrinsic to nuclear inner membrane0.0141261637694952
GO:0005639integral to nuclear inner membrane0.0141261637694952
GO:0004311farnesyltranstransferase activity0.0141261637694952
GO:0051298centrosome duplication0.0211845680019452
GO:0007098centrosome cycle0.0346376062360266
GO:0005637nuclear inner membrane0.0346376062360266
GO:0051297centrosome organization and biogenesis0.0346376062360266
GO:0031023microtubule organizing center organization and biogenesis0.0346376062360266
GO:0004659prenyltransferase activity0.0370348186593884



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
leukocyte8.14e-44140
hematopoietic lineage restricted progenitor cell5.14e-34124
nongranular leukocyte1.20e-32119
hematopoietic stem cell8.80e-32172
angioblastic mesenchymal cell8.80e-32172
hematopoietic cell8.53e-31182
hematopoietic oligopotent progenitor cell3.04e-28165
hematopoietic multipotent progenitor cell3.04e-28165
CD14-positive, CD16-negative classical monocyte9.64e-2542
classical monocyte2.58e-2345
lymphocyte6.11e-1953
common lymphoid progenitor6.11e-1953
lymphoid lineage restricted progenitor cell6.20e-1952
myeloid leukocyte1.70e-1876
granulocyte monocyte progenitor cell1.27e-1571
myeloid lineage restricted progenitor cell3.02e-1470
macrophage dendritic cell progenitor2.09e-1365
mesenchymal cell6.65e-13358
monopoietic cell1.82e-1263
monocyte1.82e-1263
monoblast1.82e-1263
promonocyte1.82e-1263
connective tissue cell1.96e-12365
myeloid cell2.78e-11112
common myeloid progenitor2.78e-11112
multi fate stem cell3.60e-10430
mature alpha-beta T cell1.29e-0918
alpha-beta T cell1.29e-0918
immature T cell1.29e-0918
mature T cell1.29e-0918
immature alpha-beta T cell1.29e-0918
T cell2.53e-0925
pro-T cell2.53e-0925
somatic stem cell4.42e-09436
lymphocyte of B lineage5.01e-0924
pro-B cell5.01e-0924
stem cell7.51e-09444
motile cell1.83e-08390
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.58e-20102
blood island3.58e-20102
hemolymphoid system1.15e-17112
bone element1.42e-1486
bone marrow1.63e-1480
connective tissue1.26e-11375
skeletal element1.32e-10101
skeletal system1.32e-10101
immune system8.08e-10115


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#46792.929979286001140.003459886809897840.0175820902364208
BATF#10538103.530116201783140.000500576618975510.00441179084465682
BCL11A#53335135.344969802128877.78734682833008e-073.41723830001666e-05
BHLHE40#855363.901896830171950.004421081584707160.0209421870294463
CEBPB#1051212.426001451337997.2620952890207e-050.0011415502256021
CTCF#10664231.786752124358340.002638113981790680.0145832840811008
E2F1#1869231.635796404959770.008155161400387650.0322022345455437
E2F4#1874132.38673600143040.002661923841356910.0146876935792199
E2F6#1876251.817810047716440.001213672086548960.00816876323046252
EBF1#1879283.614218430491773.90933375729495e-103.86635329808833e-08
EGR1#1958251.807311266235560.001322498807340150.00885047116107895
ELF1#1997342.098193197093572.75192663684192e-069.529458422584e-05
ELK4#2005133.058896544349050.0002701899502686620.00288472380046093
EP300#2033262.55249978089572.49064759389749e-068.77896537492609e-05
FOS#2353283.651344183319473.08733315870661e-103.11233578921003e-08
GATA1#2623193.733997894669693.80272468776927e-071.8602002982011e-05
GATA2#2624183.324764800057564.34737858923899e-060.0001362652678516
GATA3#262593.552589090070350.0009336924735302280.00676709980867616
HEY1#23462261.52236068290940.01169692738502120.0427018805636264
JUN#3725193.445561661657831.28287902208559e-065.12753931066196e-05
JUNB#372683.54905885910970.001833710439933230.0108535497101834
JUND#3727181.824694941357660.007161862100750310.0297418472281308
MAX#4149211.963821241871730.001339801479468540.00887583423496444
MEF2A#4205133.531333359788016.50117161038365e-050.00105611426631958
MEF2C#420874.191006977512590.001410684529980280.0091703275007227
MYC#4609241.816445868385880.001616258123115010.0101266052024722
NFKB1#4790372.94287458978514.02509809901318e-114.5892709646598e-09
NR3C1#2908122.604004057595310.001932706526537830.0113577502208578
PAX5#5079282.706490360477962.38113751652828e-071.24966643763164e-05
PBX3#509092.858414698270970.00406795865392320.0194574551800818
POLR2A#5430611.898473098116563.50287982970031e-135.17450164828954e-11
POU2F2#5452222.903401873483122.57629888629826e-069.0564146545306e-05
RAD21#5885152.25109432509920.002133102817068560.0123273088264621
REST#5978152.097832329593050.004195809344863610.0199847736657186
SIN3A#25942302.351689011658751.52938356902323e-065.86155194734741e-05
SMARCB1#659892.380789014933580.0128126164679720.0460981414943683
SMARCC1#659974.429616162861160.001027128930739080.00727664620794048
SMC3#9126112.398467554989290.005628901278100250.0254437057166636
SPI1#6688252.972580981348812.47925120131832e-071.29013710121816e-05
SRF#6722132.599468368234520.001245295201009280.00837405096247557
STAT3#6774203.049120289030214.11662223410668e-060.000130679607753151
TAF1#6872341.647298169787540.0005685007896298530.0048464332681538
TBP#6908371.987688629312552.55545666710079e-068.98919969199526e-05
TCF12#6938162.465962875869320.000553963844172540.00472945556458235
TCF7L2#6934162.49743224652460.0004817039444533670.00438419854072028
TFAP2A#7020122.872805977920860.0008346481064406040.0062974868941302
USF2#7392152.824390735884690.0002029817813352380.00241037114961579
WRNIP1#5689746.366374744891370.003703875293557920.0186837824470583
YY1#7528261.850586079655080.0006916200882168230.00557518604455671
ZNF263#10127192.263985378307290.0004374597961148270.00407745324823172



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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C213&oldid=2136783"