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|fonse_treatment=FF:0000343,FF:0011132,FF:11898-125E8
|fonse_treatment=FF:0000343,FF:0011132,FF:11898-125E8
|fonse_treatment_closure=FF:0000343,FF:0011132,FF:11898-125E8
|fonse_treatment_closure=FF:0000343,FF:0011132,FF:11898-125E8
|top_motifs=
|top_motifs=ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.81113412958;E2F1..5:1.55887653721;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.47173407883;ESRRA:1.45948202654;HES1:1.42465093997;ELK1,4_GABP{A,B1}:1.33940202614;FOXM1:1.23570658031;PPARG:1.21525038421;NR5A1,2:1.20291547788;NKX3-1:1.14199373793;YY1:1.11206075823;HIF1A:1.07259181867;FOXQ1:0.954409189296;NRF1:0.919731387698;FOXD3:0.913945025778;PAX1,9:0.895583898103;bHLH_family:0.856675919542;FOXN1:0.849993754164;ZNF143:0.812941503169;NFY{A,B,C}:0.797567402886;NKX3-2:0.75033033735;NR6A1:0.740540017465;MYB:0.734561090004;PAX5:0.66716543326;EP300:0.660351899876;HNF4A_NR2F1,2:0.657038387387;HOX{A6,A7,B6,B7}:0.630400687809;ARID5B:0.603734237799;GCM1,2:0.58328398655;SNAI1..3:0.561726623193;POU1F1:0.533437110113;TEAD1:0.494608671317;ZEB1:0.483987523372;RXR{A,B,G}:0.469254004949;TEF:0.449300045366;UFEwm:0.416767861943;TBX4,5:0.399100345744;IKZF2:0.376031041741;ALX4:0.375567018453;IKZF1:0.355395855371;TP53:0.310618185392;TFDP1:0.293259076887;ZNF148:0.291388482649;VSX1,2:0.265887391445;GFI1:0.262221880856;IRF7:0.251869745759;NFE2L1:0.2373357053;MYBL2:0.217230318901;MYOD1:0.211328955085;CREB1:0.18011213865;PAX8:0.169293828596;FOX{F1,F2,J1}:0.159103352635;PAX2:0.158765506716;HOXA9_MEIS1:0.153521644243;PAX3,7:0.151395861902;ZNF423:0.150592099479;GTF2A1,2:0.136961998917;HSF1,2:0.118060717085;HLF:0.105661484174;SOX{8,9,10}:0.0867814745119;POU2F1..3:0.063941702434;LEF1_TCF7_TCF7L1,2:0.0523401162688;POU3F1..4:0.0514606776281;NKX6-1,2:0.0406164091583;EN1,2:0.0391986169529;ZNF384:0.030292662494;CUX2:0.0286196011096;BREu{core}:0.028155098335;FOXL1:0.0230669443994;MTF1:0.022526942366;PBX1:0.00427195997494;OCT4_SOX2{dimer}:-0.00106720468208;GZF1:-0.0091689532131;ONECUT1,2:-0.0098655800205;BACH2:-0.0106397640603;RFX2..5_RFXANK_RFXAP:-0.0213647167533;NFE2:-0.0257117233998;GFI1B:-0.028185744269;CDX1,2,4:-0.0328355403449;T:-0.036341309207;HNF1A:-0.0411190480721;HOX{A5,B5}:-0.0415100812151;ZBTB16:-0.0553816064921;PDX1:-0.0626477512682;PITX1..3:-0.0668511558713;LHX3,4:-0.0928654404592;ATF5_CREB3:-0.118105605029;NFE2L2:-0.123252028748;CDC5L:-0.123552930073;CEBPA,B_DDIT3:-0.130918348727;FOS_FOS{B,L1}_JUN{B,D}:-0.135213028528;LMO2:-0.137087833807;HAND1,2:-0.147840635885;RORA:-0.173355874028;ZBTB6:-0.175943146638;TLX1..3_NFIC{dimer}:-0.177787592942;HBP1_HMGB_SSRP1_UBTF:-0.197692426712;HOX{A4,D4}:-0.198085186395;AIRE:-0.199003081949;TBP:-0.21325204569;NR3C1:-0.21571539977;MEF2{A,B,C,D}:-0.216380165317;PRRX1,2:-0.21675168697;DBP:-0.220301356153;EBF1:-0.224301558997;AHR_ARNT_ARNT2:-0.238361604249;GLI1..3:-0.24049273376;FOX{I1,J2}:-0.241193935338;RBPJ:-0.252238836029;ELF1,2,4:-0.253948603651;ATF4:-0.262622783289;BPTF:-0.284545217424;ESR1:-0.297948371135;RXRA_VDR{dimer}:-0.29925429723;STAT5{A,B}:-0.300466308723;NR1H4:-0.323274318393;STAT2,4,6:-0.328548052308;HMGA1,2:-0.330411128047;HIC1:-0.333775322085;KLF4:-0.344790789618;NFKB1_REL_RELA:-0.34530475251;PAX6:-0.345973966543;TFCP2:-0.356765332881;IRF1,2:-0.366033269522;FOSL2:-0.373490094165;SREBF1,2:-0.416061200755;EVI1:-0.416465616443;NKX2-2,8:-0.417831966219;MAFB:-0.423383399327;POU5F1:-0.432657567275;GTF2I:-0.447873645191;ALX1:-0.449186454345;CRX:-0.453188456033;TFAP2B:-0.45426743045;NANOG:-0.492911016065;ATF6:-0.496425042191;TFAP2{A,C}:-0.503294206483;NFIL3:-0.505562358075;SPIB:-0.527699440577;ADNP_IRX_SIX_ZHX:-0.532051711049;PAX4:-0.532716091198;ZFP161:-0.532939375103;TOPORS:-0.539826399698;FOXP1:-0.540487915126;RFX1:-0.547994545219;ZIC1..3:-0.572254351813;FOXP3:-0.582719523694;GATA6:-0.586247749802;JUN:-0.596715964983;REST:-0.625099480933;TFAP4:-0.629078680587;SOX2:-0.635763860941;SPI1:-0.657503578337;RUNX1..3:-0.659190899727;AR:-0.668275676277;MTE{core}:-0.672176513714;SP1:-0.67902173085;GATA4:-0.679363979277;ZNF238:-0.701805652999;SOX5:-0.703635740595;NKX2-1,4:-0.71166204239;POU6F1:-0.712114863124;SRF:-0.713533613459;NHLH1,2:-0.714732773131;SOX17:-0.71649009325;ETS1,2:-0.757663525027;MED-1{core}:-0.763329525372;NKX2-3_NKX2-5:-0.772452152221;XCPE1{core}:-0.790100750975;EGR1..3:-0.797428948932;NFATC1..3:-0.816318892712;TAL1_TCF{3,4,12}:-0.822806656297;FOXA2:-0.86314736494;STAT1,3:-0.914576274987;RREB1:-0.915212141624;MAZ:-0.926099845247;DMAP1_NCOR{1,2}_SMARC:-0.940622499065;FOXO1,3,4:-0.956362745981;ATF2:-0.996103673745;FOX{D1,D2}:-1.01953179509;HMX1:-1.08913157666;NFIX:-1.10739904696;XBP1:-1.13413760699;SMAD1..7,9:-1.13897605366;MZF1:-1.14911943214;MYFfamily:-1.15486888765;PATZ1:-1.18976847146;TGIF1:-1.20973153118;PRDM1:-1.26997636178;TLX2:-1.42096107605;SPZ1:-1.52122848801;NANOG{mouse}:-1.54264331862
|comment=
|comment=
|created_by=
|created_by=

Revision as of 17:44, 14 March 2012


Name:Hep-2 cells mock treated, biol_rep1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
age56
cell typeunclassifiable
cell lineHep-2
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3a
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: CNhs13479



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: CNhs13479



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: CNhs13479


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
4 (disease)

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