Personal tools

FF:10051-101G6: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 66: Line 66:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|top_motifs=MEF2{A,B,C,D}:6.60511133497;NR5A1,2:5.71443057427;NFE2L1:5.2570888775;ESRRA:5.14425973344;NR1H4:3.91857820306;AR:3.04951683095;HAND1,2:2.84178352375;PDX1:2.64648598035;PPARG:2.53189398697;RXR{A,B,G}:2.48544646139;MAFB:2.38312091952;GCM1,2:2.24876271746;TFAP2{A,C}:2.17261534761;RORA:2.16794280894;SRF:2.08276432413;TFAP4:1.91128075799;TGIF1:1.89793266428;IKZF2:1.82368715863;EP300:1.72309919328;RBPJ:1.70225463657;NKX2-2,8:1.65676982012;SMAD1..7,9:1.6047034741;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.58523217785;SPZ1:1.54496846265;HOX{A4,D4}:1.53336734006;NR6A1:1.46261356741;MYOD1:1.44344134964;HMX1:1.43117093061;TFCP2:1.42147049447;UFEwm:1.4004230992;TBX4,5:1.38376908668;ZNF423:1.35598857558;RXRA_VDR{dimer}:1.35392114194;IKZF1:1.32459433701;NFIX:1.30677927671;MTF1:1.27317552871;GTF2A1,2:1.26157544692;GATA4:1.23099393406;EN1,2:1.20517276122;LMO2:1.19411804979;NHLH1,2:1.18299453873;KLF4:1.17540546962;GATA6:1.16846550407;CUX2:1.15836547743;TLX1..3_NFIC{dimer}:1.15115859568;HIC1:1.08241631664;XBP1:1.05267674851;NANOG:1.02651727703;FOXL1:1.02272110148;NFATC1..3:1.02145581019;RREB1:1.01827410485;PAX6:0.97352330627;T:0.972754674815;TEAD1:0.950517342577;SOX5:0.935481639274;ESR1:0.879683233578;GLI1..3:0.863187227663;GFI1B:0.847783452919;ZNF238:0.840930173424;TBP:0.801757737252;TFAP2B:0.759658371801;MYBL2:0.707607871538;PATZ1:0.687983177899;SP1:0.64204827305;REST:0.590365216206;ZNF148:0.562974196173;FOX{D1,D2}:0.5616181126;HNF4A_NR2F1,2:0.559068352055;NR3C1:0.544295425657;YY1:0.527523916017;JUN:0.506690124368;FOXO1,3,4:0.494753126296;EBF1:0.447276716332;MTE{core}:0.42818099324;TLX2:0.428162467662;MAZ:0.396010949198;SNAI1..3:0.339343419848;SREBF1,2:0.312411976098;PAX1,9:0.304606378319;MED-1{core}:0.298946883203;EVI1:0.290233093608;PAX5:0.237442250208;GTF2I:0.195676798876;ZFP161:0.188647549161;ZIC1..3:0.146360957856;NKX3-2:0.140244511813;HSF1,2:0.125073232539;GZF1:0.12473291715;PBX1:0.0968934918771;HOX{A5,B5}:0.076416283502;FOSL2:0.0697598545966;EGR1..3:0.0549196321164;TOPORS:0.0426861831709;MYFfamily:0.0423033772413;ZEB1:0.0404380671064;HNF1A:0.0261485495031;ATF2:0.0194830016567;STAT2,4,6:-0.0213415977302;FOXP3:-0.0428944813867;IRF7:-0.0720899590172;BPTF:-0.0725458467864;ETS1,2:-0.0946077452473;ZBTB6:-0.0972509919913;NKX6-1,2:-0.0981077765589;SOX{8,9,10}:-0.119937509495;STAT5{A,B}:-0.122287881846;LEF1_TCF7_TCF7L1,2:-0.14573521511;CEBPA,B_DDIT3:-0.167533084228;ATF6:-0.179088332904;MZF1:-0.237318411015;FOXQ1:-0.26399143668;ATF4:-0.276342748844;BREu{core}:-0.276645853724;XCPE1{core}:-0.295405746442;CDX1,2,4:-0.323563360553;POU3F1..4:-0.325135871586;TP53:-0.326296988486;ATF5_CREB3:-0.333876301832;FOXA2:-0.335513231153;STAT1,3:-0.339912502914;PITX1..3:-0.362041106564;FOX{F1,F2,J1}:-0.369756261406;POU6F1:-0.38658982349;SOX17:-0.388475924283;PRDM1:-0.392163159771;FOX{I1,J2}:-0.41018223875;LHX3,4:-0.415849931951;SPI1:-0.423553717289;HLF:-0.516094381792;ALX1:-0.534702120858;NFE2:-0.547248857689;SPIB:-0.578072171219;NANOG{mouse}:-0.589915083674;ZNF143:-0.595854851037;ARID5B:-0.599624194082;NFKB1_REL_RELA:-0.604113449462;NKX2-1,4:-0.606676384561;GFI1:-0.610548478176;PAX2:-0.618123004075;CREB1:-0.623523350851;CDC5L:-0.624485039569;BACH2:-0.627114460286;RFX2..5_RFXANK_RFXAP:-0.668303662622;VSX1,2:-0.675021736944;NFE2L2:-0.683183585607;bHLH_family:-0.701795303013;HOX{A6,A7,B6,B7}:-0.70431168481;HES1:-0.724339851285;FOXP1:-0.753620788791;FOS_FOS{B,L1}_JUN{B,D}:-0.766769628978;NRF1:-0.781796152106;FOXN1:-0.806042844586;IRF1,2:-0.817689447419;POU1F1:-0.857581565547;RFX1:-0.862809783699;ALX4:-0.899540208;NFY{A,B,C}:-0.925449060313;NFIL3:-0.933083480945;RUNX1..3:-0.939633547676;DMAP1_NCOR{1,2}_SMARC:-0.990763421783;ELF1,2,4:-1.01382927899;TEF:-1.12793904438;HOXA9_MEIS1:-1.12954138287;FOXM1:-1.154437941;ZBTB16:-1.17931520253;POU2F1..3:-1.29501300641;FOXD3:-1.31569382882;E2F1..5:-1.35412770957;ONECUT1,2:-1.37937790154;TFDP1:-1.40045027241;TAL1_TCF{3,4,12}:-1.43319288745;NKX3-1:-1.49113420586;ZNF384:-1.51895947675;OCT4_SOX2{dimer}:-1.5814283301;HMGA1,2:-1.58340360183;NKX2-3_NKX2-5:-1.60099431411;PRRX1,2:-1.6419702384;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.65538063175;PAX4:-1.6588576268;PAX3,7:-1.68128359077;SOX2:-1.75362689017;ADNP_IRX_SIX_ZHX:-1.79745116402;AHR_ARNT_ARNT2:-1.81355960385;ELK1,4_GABP{A,B1}:-1.82435114277;HIF1A:-1.92721270506;MYB:-1.97101636593;CRX:-2.00426124264;HBP1_HMGB_SSRP1_UBTF:-2.08330914172;DBP:-2.23092158391;AIRE:-2.23276251431;PAX8:-2.26625257679;POU5F1:-2.43093037091
|comment=
|comment=
|created_by=
|created_by=

Revision as of 17:58, 14 March 2012


Name:heart, adult, diseased, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueheart
dev stage92 years old adult
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3040792
catalog numberCat:636581
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]





Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11758



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11758



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs11758


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0001009 (circulatory system)
0001062 (anatomical entity)
0007023 (adult organism)
0007100 (primary circulatory organ)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA