Personal tools

FF:13469-144I4: 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=TFDP1:1.89856963808;PAX8:1.62016126467;VSX1,2:1.43753377083;NKX2-1,4:1.22846100682;SPZ1:1.18059145387;PDX1:1.14822026271;TFAP4:1.14485598029;TFAP2{A,C}:1.13090384768;HOX{A4,D4}:1.06979267821;TLX1..3_NFIC{dimer}:1.00028470519;LEF1_TCF7_TCF7L1,2:0.983029651897;NFIX:0.948128957041;PAX1,9:0.875659511033;POU1F1:0.862905818614;ZNF384:0.848743210514;POU6F1:0.846853910981;SRF:0.832346461061;TEAD1:0.832306250879;CDC5L:0.820687826483;HOX{A5,B5}:0.782424058761;GATA4:0.772139480589;NKX3-1:0.765455634911;NR6A1:0.734802481342;ADNP_IRX_SIX_ZHX:0.732125282456;GZF1:0.72897881842;MYBL2:0.71952066963;XBP1:0.716073929717;E2F1..5:0.710803682466;GFI1B:0.704375221257;POU5F1:0.691620771953;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.665219279213;HBP1_HMGB_SSRP1_UBTF:0.665056195728;TAL1_TCF{3,4,12}:0.658482192558;TFAP2B:0.623486279832;SOX17:0.620357185262;MZF1:0.59783807752;GFI1:0.58068627353;NR3C1:0.568003173838;FOXD3:0.560859237115;NKX6-1,2:0.549688802309;ZNF238:0.546832414535;NHLH1,2:0.546593169474;SOX{8,9,10}:0.495664512017;HOX{A6,A7,B6,B7}:0.482501432966;NKX2-3_NKX2-5:0.47123078206;RORA:0.46799258413;EGR1..3:0.46711387626;PAX4:0.462697580489;MTF1:0.457671437072;HIC1:0.450104679371;GTF2A1,2:0.437685443588;NFATC1..3:0.435298079314;POU3F1..4:0.427135015925;KLF4:0.424698064309;PRDM1:0.422927697481;LHX3,4:0.416455829932;AR:0.397898443029;SOX2:0.397594078796;NR5A1,2:0.376827138042;ZFP161:0.362087832062;PRRX1,2:0.361477353832;GCM1,2:0.349643398442;TBX4,5:0.342015462503;NFE2L2:0.3393949418;FOSL2:0.333070841417;GTF2I:0.328853581988;TFCP2:0.32800740858;AHR_ARNT_ARNT2:0.299346400358;FOS_FOS{B,L1}_JUN{B,D}:0.281339144432;MTE{core}:0.269890565055;ALX1:0.262769144462;MEF2{A,B,C,D}:0.259843546333;EN1,2:0.235520050447;EVI1:0.206112556071;HSF1,2:0.195215021301;RFX1:0.17602663817;JUN:0.172240188357;GLI1..3:0.158131296853;HOXA9_MEIS1:0.148273032364;DMAP1_NCOR{1,2}_SMARC:0.145240452296;NFIL3:0.144018051762;CDX1,2,4:0.139037031145;BACH2:0.138969408122;BREu{core}:0.130702007369;CUX2:0.130642108112;MED-1{core}:0.130297223201;PBX1:0.120190774644;HNF1A:0.117558380323;CREB1:0.116090436069;RUNX1..3:0.113843248645;NRF1:0.065002395393;MYFfamily:0.0518722862867;MAZ:0.0510232344968;PPARG:0.0316367669214;TBP:0.0270316961337;HES1:0.0167671469549;FOXA2:0.00370975662904;NFE2:0.000531981769745;ATF6:-0.00959715843629;ZBTB6:-0.0111879628477;STAT2,4,6:-0.0148607252273;ZNF148:-0.01628383406;REST:-0.023311300532;RXR{A,B,G}:-0.024701761489;HNF4A_NR2F1,2:-0.0253162679424;PATZ1:-0.0336231249589;ZNF143:-0.0374688883707;PAX3,7:-0.0550549728123;MYB:-0.059037618476;ZIC1..3:-0.066719414247;NANOG{mouse}:-0.0715307512227;NFE2L1:-0.0749399921209;RREB1:-0.078156650156;SMAD1..7,9:-0.0881781375427;PAX6:-0.103891217885;T:-0.104911737981;HLF:-0.105517317374;RFX2..5_RFXANK_RFXAP:-0.110460905229;PITX1..3:-0.114686070958;POU2F1..3:-0.1171092422;TGIF1:-0.129774230842;ONECUT1,2:-0.130720996106;FOXQ1:-0.133783999198;EBF1:-0.141004823111;GATA6:-0.142239157628;NFY{A,B,C}:-0.152213642602;ALX4:-0.15272455523;HAND1,2:-0.179424009605;STAT5{A,B}:-0.187073435079;RXRA_VDR{dimer}:-0.217261256712;TP53:-0.231773890931;SREBF1,2:-0.235577140498;ZBTB16:-0.237448427982;DBP:-0.249183474998;NR1H4:-0.249247022401;CEBPA,B_DDIT3:-0.257016707543;MAFB:-0.288689058761;CRX:-0.307177980075;XCPE1{core}:-0.327550089022;ZNF423:-0.346743001445;NFKB1_REL_RELA:-0.360679054645;FOXO1,3,4:-0.383384675623;HMGA1,2:-0.390455252776;ESRRA:-0.395060654534;OCT4_SOX2{dimer}:-0.396381445804;IKZF1:-0.421172704069;IKZF2:-0.429629454119;SPIB:-0.437721526994;NANOG:-0.446394329188;IRF1,2:-0.451106865018;IRF7:-0.456418872036;ESR1:-0.46954647759;ETS1,2:-0.491011315717;SOX5:-0.491558719608;FOX{F1,F2,J1}:-0.522369406268;PAX5:-0.522857863683;SPI1:-0.525478333858;NKX3-2:-0.548355791856;UFEwm:-0.550278224169;LMO2:-0.578799488183;PAX2:-0.61254460971;ATF5_CREB3:-0.619661934575;HMX1:-0.63255983154;bHLH_family:-0.637078557737;FOXL1:-0.648098744478;FOXP3:-0.654397225454;SP1:-0.655061070144;ATF2:-0.664965541517;ELK1,4_GABP{A,B1}:-0.66789876379;AIRE:-0.67910407151;ELF1,2,4:-0.7007750003;FOX{I1,J2}:-0.738753633407;FOX{D1,D2}:-0.740712898543;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.747096089992;TLX2:-0.747542389551;ZEB1:-0.765725959467;ATF4:-0.768632370075;FOXN1:-0.771298445866;MYOD1:-0.827986121122;YY1:-0.833305591566;SNAI1..3:-0.868867124884;HIF1A:-0.887300714656;FOXP1:-0.909876929442;FOXM1:-0.962700056335;STAT1,3:-0.969337924819;BPTF:-0.970227966435;ARID5B:-0.970966808869;NKX2-2,8:-0.981137292406;TEF:-1.02228248004;TOPORS:-1.04138959857;RBPJ:-1.07822938386;EP300:-1.15783808773
|comment=
|comment=
|created_by=
|created_by=

Revision as of 17:47, 14 March 2012


Name:Myoblast differentiation to myotubes, day00, control donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskeletal muscle
dev stageNA
sexfemale
age3 years old
cell typemyoblast
cell lineNA
companyNA
collaborationBeatrice Bodega/Valerio Orlando
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
CollapseHg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
CollapseHg38
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: CNhs13847



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: CNhs13847



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: CNhs13847


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

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