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Coexpression cluster:C22

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Full id: C22_CD4_CD8_Natural_Basophils_CD14_Peripheral_CD19



Phase1 CAGE Peaks


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


p.valueFDRnGenesnPathwayName
3.07051124390401e-070.00019436336173912412433IL-2 up reg. targets (Netpath):NetPath_14



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:0043229intracellular organelle2.38049931056861e-08
GO:0043226organelle2.38049931056861e-08
GO:0043231intracellular membrane-bound organelle2.38049931056861e-08
GO:0043227membrane-bound organelle2.38049931056861e-08
GO:0044424intracellular part4.33330089415057e-08
GO:0016070RNA metabolic process4.84664175355703e-08
GO:0044446intracellular organelle part1.18579757723832e-06
GO:0044422organelle part1.18579757723832e-06
GO:0005634nucleus1.22193353533065e-06
GO:0005622intracellular1.72136955155334e-06
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process4.5361807911798e-06
GO:0031323regulation of cellular metabolic process4.5361807911798e-06
GO:0005515protein binding4.5361807911798e-06
GO:0019222regulation of metabolic process4.5361807911798e-06
GO:0010467gene expression5.08415557532658e-06
GO:0010468regulation of gene expression8.34105383112857e-06
GO:0043283biopolymer metabolic process9.49703305556073e-06
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process1.47185230496317e-05
GO:0006350transcription2.89338681945918e-05
GO:0006351transcription, DNA-dependent3.85069121523815e-05
GO:0032774RNA biosynthetic process3.85069121523815e-05
GO:0045449regulation of transcription3.89451633936155e-05
GO:0050789regulation of biological process5.28644558462554e-05
GO:0050794regulation of cellular process6.07645703717158e-05
GO:0006355regulation of transcription, DNA-dependent8.33397843019912e-05
GO:0065007biological regulation8.33397843019912e-05
GO:0016043cellular component organization and biogenesis0.000939806489727041
GO:0044428nuclear part0.00105857407289522
GO:0043170macromolecule metabolic process0.00274682983113233
GO:0044237cellular metabolic process0.00309627480861559
GO:0044464cell part0.00412853932711923
GO:0006366transcription from RNA polymerase II promoter0.00436943806518212
GO:0006396RNA processing0.00584637465326544
GO:0000228nuclear chromosome0.00646726516320833
GO:0033239negative regulation of amine metabolic process0.00646726516320833
GO:0045763negative regulation of amino acid metabolic process0.00646726516320833
GO:0001933negative regulation of protein amino acid phosphorylation0.00646726516320833
GO:0044238primary metabolic process0.00716634198538681
GO:0016049cell growth0.00919660848647982
GO:0005737cytoplasm0.00978630992518552
GO:0008361regulation of cell size0.00978630992518552
GO:0003707steroid hormone receptor activity0.0102750781499155
GO:0032502developmental process0.0134382949356823
GO:0065008regulation of biological quality0.0139482538859029
GO:0006996organelle organization and biogenesis0.0151495845376302
GO:0030004cellular monovalent inorganic cation homeostasis0.0188293926232484
GO:0055067monovalent inorganic cation homeostasis0.0188293926232484
GO:0016455RNA polymerase II transcription mediator activity0.0210293445334764
GO:0012505endomembrane system0.0222344919942081
GO:0019903protein phosphatase binding0.0228347197383268
GO:0004879ligand-dependent nuclear receptor activity0.0230510638845802
GO:0016072rRNA metabolic process0.0274179711205959
GO:0003702RNA polymerase II transcription factor activity0.0293637126013609
GO:0017124SH3 domain binding0.0293637126013609
GO:0019902phosphatase binding0.0342893265491958
GO:0000119mediator complex0.0342893265491958
GO:0009892negative regulation of metabolic process0.0361207774297424
GO:0005496steroid binding0.0364892766763437
GO:0044444cytoplasmic part0.0364892766763437
GO:0003712transcription cofactor activity0.0366098248388845
GO:0016563transcription activator activity0.0378988578829624
GO:0006695cholesterol biosynthetic process0.0378988578829624
GO:0005795Golgi stack0.0378988578829624
GO:0008033tRNA processing0.0378988578829624
GO:0003723RNA binding0.0378988578829624
GO:0035026leading edge cell differentiation0.0378988578829624
GO:0048388endosomal lumen acidification0.0378988578829624
GO:0001667ameboidal cell migration0.0378988578829624
GO:0047757chondroitin-glucuronate 5-epimerase activity0.0378988578829624
GO:0000782telomere cap complex0.0378988578829624
GO:0035030phosphoinositide 3-kinase complex, class IA0.0378988578829624
GO:0000783nuclear telomere cap complex0.0378988578829624
GO:0008455alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity0.0378988578829624
GO:0004883glucocorticoid receptor activity0.0378988578829624
GO:0048244phytanoyl-CoA dioxygenase activity0.0378988578829624
GO:0032027myosin light chain binding0.0378988578829624
GO:0000902cell morphogenesis0.0415393574255019
GO:0032989cellular structure morphogenesis0.0415393574255019



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
mature alpha-beta T cell2.53e-3118
alpha-beta T cell2.53e-3118
immature T cell2.53e-3118
mature T cell2.53e-3118
immature alpha-beta T cell2.53e-3118
leukocyte1.09e-27136
CD4-positive, alpha-beta T cell2.42e-226
hematopoietic stem cell5.12e-22168
angioblastic mesenchymal cell5.12e-22168
T cell1.16e-2125
pro-T cell1.16e-2125
hematopoietic lineage restricted progenitor cell1.48e-21120
nongranular leukocyte2.31e-21115
lymphoid lineage restricted progenitor cell1.75e-2052
hematopoietic cell2.02e-20177
lymphocyte5.29e-2053
common lymphoid progenitor5.29e-2053
nucleate cell4.27e-1955
hematopoietic oligopotent progenitor cell8.48e-18161
hematopoietic multipotent progenitor cell8.48e-18161
CD8-positive, alpha-beta T cell7.48e-1511
natural killer cell2.84e-123
pro-NK cell2.84e-123
naive T cell7.57e-123
basophil2.81e-113
single nucleate cell3.59e-113
mononuclear cell3.59e-113
intermediate monocyte2.42e-099
CD14-positive, CD16-positive monocyte2.42e-099
regulatory T cell2.22e-082
CD4-positive, CD25-positive, alpha-beta regulatory T cell2.22e-082
naive regulatory T cell2.22e-082
myeloid leukocyte6.71e-0772
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.35e-0798
blood island1.35e-0798


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
BATF#10538642.032463252552061.09371172539299e-076.37067255372664e-06
BCL11A#53335782.885029332570211.64022379248222e-163.26914756990554e-14
BCL3#602421.891757911026098.56751201934674e-050.00128449955180671
BCLAF1#9774681.919661065825663.40351641451693e-071.68864537204624e-05
BRCA1#672701.842107099120819.84944292264352e-074.17647571822154e-05
CCNT2#9051571.296979983811130.0003298836898940680.00336091334395147
CEBPB#10511521.579679842405967.87787551786444e-096.08548403262015e-07
CHD2#11061051.416065707408440.0002011351514190870.00239116153432647
CTCF#106641941.355788443776473.24930284579627e-060.000109046895858649
CTCFL#140690591.518959566074950.001136532288160780.00778196391812912
E2F1#18692311.477975109044491.04566831683246e-101.13052332651827e-08
E2F4#1874851.403891951498280.001085614360153460.00765929056002618
E2F6#18762201.439079870891043.95361688396425e-093.24106588496344e-07
EBF1#18791922.229519732126798.79894825779481e-273.02287288518366e-24
EGR1#19582241.456782421430868.84633747676367e-108.2712859421282e-08
ELF1#19973111.726556017195766.55530514038116e-262.15292299860462e-23
ELK4#2005701.481744088778050.0007768278938049430.00608909699798067
EP300#20331691.492563431201724.73172927183485e-083.07515291487965e-06
ETS1#21131161.471364102966721.79643594058463e-050.000409288772248513
FOS#23531271.489883082437543.6385265953531e-060.000119460571861705
FOSL1#8061311.605112087623940.007762899045765270.0319242956938368
FOSL2#2355641.412689489820010.003864309236630920.0190567849827414
FOXA1#31691291.863758993051795.73780392445766e-127.45336447843823e-10
FOXA2#3170581.862538328102466.2823113041017e-060.000185501359991257
GABPB1#25531711.575715692290947.90832650876659e-107.46779124999163e-08
GATA1#26231232.174599611065785.12783234953315e-169.9175126435721e-14
GATA2#26241031.711509737361238.18139838769712e-084.88261180692971e-06
GTF2B#2959542.248978900200144.98163435016177e-083.19188288280089e-06
GTF2F1#29621021.694192189607931.54163595440607e-078.64234661525582e-06
HDAC8#558691010.12495480591198.11629135605151e-084.85207414387329e-06
HEY1#234622611.374796587028155.17990097594802e-094.15502056856402e-07
HMGN3#93241361.450172738429836.10422627655217e-060.0001815776952711
HNF4A#3172501.507971992369860.003046204810563760.0160694304581507
IRF1#36591421.413920799225651.32828466925563e-050.000324350532084144
IRF4#3662822.342881408491551.76548915291261e-122.4165913714422e-10
JUN#37251111.810852725357671.14374388907224e-091.04966140624619e-07
JUNB#3726401.596382407291850.003004134179654170.0159652335430949
JUND#37271641.495599591221457.01607330078933e-084.25276656680868e-06
MAFF#23764231.688726465800180.01170073481372910.0427142872246864
MAX#41492231.876036347468821.27121898778693e-213.44843739910335e-19
MEF2A#4205982.394832632522972.42228715712596e-154.38442371582457e-13
MEF2C#4208371.992855431847578.08995317935978e-050.00122610161094058
MXI1#46011702.207910269738045.02410743120218e-231.47806410142908e-20
MYC#46092371.613664672192214.48240858107969e-157.9211213164024e-13
NFKB1#47903122.232432579333091.04908077339574e-477.11460694108295e-45
NFYA#4800641.537466968434360.0005232519362519030.00453246321391827
NFYB#4801771.682534655179027.52541198926354e-060.000214915641987064
NR3C1#2908761.483637253154040.0004471951729959140.00416150910385104
NRF1#4899981.560113932041299.29675565791356e-060.000247626591215719
PAX5#50792302.000000094095054.17518423075645e-261.3976027752435e-23
PBX3#5090772.200022786022551.61552405150297e-101.69913108172123e-08
POLR2A#54305601.567892801659093.23905362260889e-502.41631086636893e-47
POLR3A#11128104.421539896893650.0001156122211229360.0015721907242003
POU2F2#54521752.077668461675285.85929631829075e-211.54530062673224e-18
RAD21#58851031.390571696521510.0004390195667334290.00409162631894277
REST#59781121.409130659982190.0001454950532831350.00188014821453073
RFX5#59931432.246220662697397.2863875902966e-201.82053357306935e-17
SIN3A#259422681.889936253958872.30864784163372e-278.22910825707796e-25
SMARCB1#6598781.856208384524481.68424625674557e-079.28237439621375e-06
SMARCC1#6599442.504808096562954.8501767795163e-083.14235491734431e-06
SMARCC2#6601161.964127758579350.009125482367655720.0345222680115766
SP1#66672201.634477057615381.92846074008846e-143.25900503615047e-12
SPI1#66881882.010968474057724.42889250371759e-211.17696973077802e-18
SREBF1#6720382.328842605917282.2105149795929e-067.92257975132816e-05
SRF#67221142.050688816019733.45412307745709e-135.10970481708982e-11
STAT3#6774941.289217352975880.006943162159004050.0293696602966474
TAF1#68723681.603964841139855.78027931874556e-261.9164653706999e-23
TAL1#6886522.024990961182391.95624954621317e-067.1939699421464e-05
TBP#69083471.676987520759381.54031420315189e-275.56639706100278e-25
TCF12#69381391.927236794529225.93140884869317e-149.559728530072e-12
TCF7L2#69341011.418237070243640.0002550075235736060.00274479344063731
TFAP2C#7022921.2965437185230.006524479970077450.02793351494609
THAP1#55145381.554142757377250.005750761997813650.0259059624003476
TRIM28#10155711.720896060252468.37202917142854e-060.00022949248153145
USF1#73911611.335334268097116.53678146338592e-050.00106090896543055
USF2#7392961.626142045588892.16864910086632e-067.83979035809547e-05
WRNIP1#56897233.293167118690551.0289847315104e-064.32285343420009e-05
YY1#75282601.664803644018261.46851145437133e-183.34868706949972e-16
ZBTB33#10009361.486219166987380.01334279434910610.0471656151303535
ZEB1#6935952.091787538026941.46306583860881e-111.79344052955945e-09
ZNF263#101271241.329215597117760.0006379661592508380.0052306914512481



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