FF:11896-125E6: Difference between revisions
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|fonse_treatment=FF:0000625,FF:0000632,FF:0000639,FF:0011134,FF:11896-125E6 | |fonse_treatment=FF:0000625,FF:0000632,FF:0000639,FF:0011134,FF:11896-125E6 | ||
|fonse_treatment_closure=FF:0000625,FF:0000632,FF:0000639,FF:0011134,FF:11896-125E6 | |fonse_treatment_closure=FF:0000625,FF:0000632,FF:0000639,FF:0011134,FF:11896-125E6 | ||
|top_motifs= | |top_motifs=ESRRA:1.86248839871;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.7390907079;PPARG:1.63215805797;HES1:1.58500911002;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.5752529006;E2F1..5:1.56929398055;FOXM1:1.39421945517;NR5A1,2:1.28255545967;ELK1,4_GABP{A,B1}:1.18770515853;FOXQ1:1.13261384624;YY1:0.997614625131;bHLH_family:0.831316974252;FOXN1:0.754792402688;NRF1:0.740816926278;NR6A1:0.731997661223;PAX8:0.707827628405;NKX3-1:0.699796016955;MYB:0.666081308914;HOX{A6,A7,B6,B7}:0.652718517127;HIF1A:0.648179948692;NFY{A,B,C}:0.646232658876;PAX1,9:0.64410205857;PAX5:0.644101714842;HNF4A_NR2F1,2:0.639023635174;ARID5B:0.616084063431;HOXA9_MEIS1:0.602672584121;ZNF143:0.566445022769;CREB1:0.55764098358;POU1F1:0.554564454952;GCM1,2:0.523959422643;EP300:0.505362351454;NKX3-2:0.496400031793;SNAI1..3:0.469385710638;ZEB1:0.459405404609;LEF1_TCF7_TCF7L1,2:0.391784572962;IRF7:0.349794326131;TBX4,5:0.339978860671;IKZF1:0.33748103118;ALX1:0.322842375428;GFI1:0.319898193415;FOX{F1,F2,J1}:0.309981194126;FOXD3:0.307423083018;TEAD1:0.304008515469;UFEwm:0.274361973746;ZNF148:0.271024938889;PDX1:0.26669207568;MYOD1:0.265700889472;TP53:0.244284799276;PAX2:0.197703552853;ATF5_CREB3:0.18831326365;HLF:0.159038433675;NFE2L1:0.147581294606;ZBTB16:0.142496515685;VSX1,2:0.118762020676;HSF1,2:0.118435829074;GFI1B:0.111427148587;HOX{A5,B5}:0.106065640727;PAX3,7:0.105032802875;STAT5{A,B}:0.0906725838824;BACH2:0.0800196761053;NANOG:0.0622206517278;ONECUT1,2:0.0579448438128;LHX3,4:0.0560130523313;ATF6:0.0534931896222;NFE2:0.0496793575842;PAX4:0.041252383219;CUX2:0.0405113384999;RORA:0.0299556835015;OCT4_SOX2{dimer}:0.0207230402247;NR3C1:0.012279031095;ZNF423:0.000144463227079;TFDP1:-0.00254373317081;CDX1,2,4:-0.014366090772;PRRX1,2:-0.0172398188364;PITX1..3:-0.0302242377374;FOS_FOS{B,L1}_JUN{B,D}:-0.0388208617707;MYBL2:-0.0390773840808;PBX1:-0.0501136517204;ALX4:-0.0515958467604;CDC5L:-0.0562854499129;HAND1,2:-0.059875092564;HNF1A:-0.0636352481454;NFE2L2:-0.0650710439108;RXR{A,B,G}:-0.0699595740251;AHR_ARNT_ARNT2:-0.0809970546272;GTF2A1,2:-0.0818407751011;BREu{core}:-0.0880193787657;MEF2{A,B,C,D}:-0.0960019869584;HOX{A4,D4}:-0.097530679401;TBP:-0.128870249928;MAFB:-0.13421604669;ESR1:-0.137865781791;TLX1..3_NFIC{dimer}:-0.143441387458;TEF:-0.144120193483;MTF1:-0.16749102535;IKZF2:-0.180574678624;ATF4:-0.181908141354;RFX2..5_RFXANK_RFXAP:-0.199825358749;SOX{8,9,10}:-0.215058671001;NFIL3:-0.232674887838;ZBTB6:-0.244307935822;GLI1..3:-0.256826042682;LMO2:-0.257990414999;NFKB1_REL_RELA:-0.259789206718;FOXA2:-0.267238588621;FOSL2:-0.269503720913;ELF1,2,4:-0.274787949646;NKX2-2,8:-0.278810234454;NKX6-1,2:-0.284601477753;GZF1:-0.304735363647;PAX6:-0.306407427952;FOX{I1,J2}:-0.308304577953;POU3F1..4:-0.312571261033;CEBPA,B_DDIT3:-0.324760000012;T:-0.341790694616;JUN:-0.348621625835;RXRA_VDR{dimer}:-0.349147883795;NR1H4:-0.352660466046;KLF4:-0.354288787917;TFCP2:-0.361384440193;RFX1:-0.365820996854;STAT2,4,6:-0.371890423009;GATA6:-0.381746056397;EN1,2:-0.386136630658;SREBF1,2:-0.402756652526;DBP:-0.468124699849;CRX:-0.469680846239;SOX17:-0.477425436985;FOXP3:-0.480293023094;IRF1,2:-0.497234541142;BPTF:-0.51854499828;EVI1:-0.524643733645;SPIB:-0.532988890978;REST:-0.537992442169;ZFP161:-0.538681650538;EBF1:-0.549173252988;HIC1:-0.553840003838;GTF2I:-0.592896027457;POU6F1:-0.598633978513;TFAP2{A,C}:-0.600091991239;ZNF384:-0.602674728103;SPI1:-0.607914945987;POU2F1..3:-0.618322410853;RBPJ:-0.623423343977;NKX2-1,4:-0.628351551876;SOX5:-0.629245244715;AIRE:-0.636389888401;SRF:-0.644525280826;RUNX1..3:-0.714574963597;AR:-0.733633911191;TFAP4:-0.749329310444;FOXL1:-0.766126064617;FOXP1:-0.766505046527;ETS1,2:-0.778404935305;ADNP_IRX_SIX_ZHX:-0.788683521583;TFAP2B:-0.800013143371;TAL1_TCF{3,4,12}:-0.817946110633;HBP1_HMGB_SSRP1_UBTF:-0.827578125879;NHLH1,2:-0.830999368108;SP1:-0.838981653975;ZIC1..3:-0.839492205281;NFATC1..3:-0.857323076363;ATF2:-0.873550525048;MED-1{core}:-0.876171177111;HMGA1,2:-0.895567831727;GATA4:-0.901231281242;POU5F1:-0.952923916914;FOX{D1,D2}:-0.998328630513;SOX2:-1.0048757321;DMAP1_NCOR{1,2}_SMARC:-1.01193891764;RREB1:-1.03186458498;MYFfamily:-1.03526332826;TGIF1:-1.07054829679;MAZ:-1.0757838636;ZNF238:-1.12023944195;XCPE1{core}:-1.12617481611;EGR1..3:-1.14081430107;FOXO1,3,4:-1.14224191136;SMAD1..7,9:-1.15090251932;MTE{core}:-1.16996079383;XBP1:-1.170358838;NKX2-3_NKX2-5:-1.18711068592;TOPORS:-1.19851168107;PRDM1:-1.20146455297;STAT1,3:-1.34962664711;HMX1:-1.35552506957;MZF1:-1.36819348115;TLX2:-1.39672016351;NFIX:-1.40924611381;PATZ1:-1.42485524419;NANOG{mouse}:-1.45782202847;SPZ1:-1.83550848291 | ||
|comment= | |comment= | ||
|created_by= | |created_by= |
Revision as of 17:44, 14 March 2012
Name: | Hep-2 cells treated with Streptococci strain JRS4, biol_rep3 |
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Species: | Human (Homo sapiens) |
Library ID: | {{{library_id}}} |
Sample type: | {{{sample_category}}} |
Genomic View: | UCSC |
CAGEd-oPOSSUM: | link |
Additional information | ||||||||||||||||||||||||||||
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Sample information
RNA information
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Download raw sequence, BAM & CTSS | ||||||||||||
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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: CNhs13499
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: CNhs13499
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: CNhs13499
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000210 human sample
FF:0011134 human Hep-2 cells treated with Streptococci strain JRS4 sample
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