FF:10064-101I1: Difference between revisions
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|top_motifs= | |top_motifs=HNF4A_NR2F1,2:6.19298457557;HNF1A:4.35396377172;GATA6:2.44692411609;RBPJ:2.36712367089;FOXD3:2.35754038203;FOXM1:2.32039237084;NR6A1:2.31478722758;SPZ1:1.84095286303;MYBL2:1.77560342697;IKZF2:1.72616198925;ALX1:1.71798437335;SNAI1..3:1.7179629968;TBP:1.68248625693;ZNF384:1.65340371094;ONECUT1,2:1.44312003118;RREB1:1.44173143154;KLF4:1.4384009039;ZEB1:1.41986878279;SP1:1.40482681395;MTF1:1.39918513764;PRDM1:1.38228660882;NR1H4:1.34848899252;TOPORS:1.33138194345;MAZ:1.25059594765;LMO2:1.2203391431;XCPE1{core}:1.17727928914;DBP:1.12758893249;PATZ1:1.11700530071;EP300:1.11427881203;GATA4:0.993553391781;MYFfamily:0.990965321495;HIC1:0.970541479878;TFCP2:0.96356621416;SRF:0.927069379678;PAX5:0.898760144031;GCM1,2:0.897596048249;IRF1,2:0.87859079284;FOXA2:0.85715460952;ZNF423:0.83026836849;TLX2:0.820822838031;RXRA_VDR{dimer}:0.810485743723;PITX1..3:0.787355655818;HOX{A6,A7,B6,B7}:0.776539448542;NKX2-3_NKX2-5:0.751466337829;FOXL1:0.746895407493;IRF7:0.73983671579;TFAP2{A,C}:0.734017296192;POU6F1:0.728480301559;POU5F1:0.720414938347;T:0.718366106861;PBX1:0.70831080865;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.705657414328;MTE{core}:0.692886332486;MED-1{core}:0.677280593503;TEF:0.664253975122;STAT1,3:0.657772906399;SOX5:0.651587657996;ATF6:0.647341848995;TFAP2B:0.640778348585;MYOD1:0.61561329054;MZF1:0.61098379805;CDX1,2,4:0.603025382439;ALX4:0.58398965235;ESR1:0.575923196443;GTF2I:0.536637845242;NR3C1:0.528261558711;TLX1..3_NFIC{dimer}:0.521681054798;FOXP1:0.50283664952;ESRRA:0.500733644222;GFI1:0.478932780618;NANOG{mouse}:0.472433059604;ZNF148:0.45691262158;VSX1,2:0.442082879091;TAL1_TCF{3,4,12}:0.412174697209;BREu{core}:0.355656749483;UFEwm:0.354901051673;GZF1:0.345766038689;REST:0.341716286259;GLI1..3:0.271432806119;HMGA1,2:0.245878298136;SREBF1,2:0.242915439139;NKX6-1,2:0.240303286765;NKX3-2:0.235611343477;CUX2:0.221057103714;PAX6:0.212080131074;AIRE:0.209905286899;FOX{D1,D2}:0.20797040718;ZFP161:0.173269579917;ADNP_IRX_SIX_ZHX:0.166098458344;ZIC1..3:0.158685748827;TEAD1:0.1487324363;HMX1:0.146794721174;PRRX1,2:0.0894190985043;FOXP3:0.0699046965103;TFAP4:0.065322323117;SPIB:0.0538004822161;EVI1:0.0439179058776;FOX{I1,J2}:0.0427845034327;SPI1:0.0355131412123;LEF1_TCF7_TCF7L1,2:0.0291541175942;ZBTB16:0.0235171210217;EGR1..3:0.00887952320664;DMAP1_NCOR{1,2}_SMARC:0.00629939952334;RXR{A,B,G}:0.0054049256168;OCT4_SOX2{dimer}:-0.0145874558004;STAT2,4,6:-0.0165123631781;ETS1,2:-0.0268599457748;NFY{A,B,C}:-0.0379885753391;GTF2A1,2:-0.0419284918767;SOX{8,9,10}:-0.0469877178275;HAND1,2:-0.0477595308222;EBF1:-0.0559172935768;FOXQ1:-0.0591387910679;E2F1..5:-0.0606532576379;PAX3,7:-0.0606650004485;POU1F1:-0.0788975893061;NHLH1,2:-0.113884322784;NR5A1,2:-0.120608793393;IKZF1:-0.144087064044;SMAD1..7,9:-0.145719647236;GFI1B:-0.146101040508;bHLH_family:-0.154318946497;ZNF143:-0.155922889324;ZBTB6:-0.158603469804;FOXN1:-0.159442204104;PAX1,9:-0.167846757545;YY1:-0.190854168248;TBX4,5:-0.21812096307;NANOG:-0.23056881593;SOX2:-0.245519604919;LHX3,4:-0.2493803534;FOXO1,3,4:-0.253713766365;CDC5L:-0.25520618816;ZNF238:-0.27255582664;ELF1,2,4:-0.273275616578;PAX2:-0.275330652661;NFATC1..3:-0.275901398976;JUN:-0.276070994787;BPTF:-0.287133181631;ELK1,4_GABP{A,B1}:-0.343750432405;ATF4:-0.344610603511;ATF2:-0.354973692536;RUNX1..3:-0.363221842696;NKX3-1:-0.366823483722;NFKB1_REL_RELA:-0.413748336082;TP53:-0.450367401763;SOX17:-0.451346561892;EN1,2:-0.454268547891;POU3F1..4:-0.506523806669;TGIF1:-0.517745978907;TFDP1:-0.526210962265;FOX{F1,F2,J1}:-0.526854396235;PDX1:-0.531728450952;NRF1:-0.538924919007;NKX2-1,4:-0.552015998178;AR:-0.586066892545;HOX{A5,B5}:-0.588877500994;RFX1:-0.60739851248;MEF2{A,B,C,D}:-0.6324427245;AHR_ARNT_ARNT2:-0.647241458813;ARID5B:-0.672337683376;NKX2-2,8:-0.704917240011;PAX4:-0.706509380036;RORA:-0.748581417312;RFX2..5_RFXANK_RFXAP:-0.759083506253;XBP1:-0.782415878163;HLF:-0.792679536697;FOSL2:-0.798234019627;NFE2:-0.802326632081;CREB1:-0.840423206767;POU2F1..3:-0.867216816841;MAFB:-0.900498077982;NFIX:-0.960457174784;FOS_FOS{B,L1}_JUN{B,D}:-0.990735711247;ATF5_CREB3:-0.999060113112;BACH2:-1.00455639721;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.04799464115;NFE2L2:-1.0493744689;MYB:-1.10030413001;CRX:-1.13601247645;CEBPA,B_DDIT3:-1.1843794404;HOXA9_MEIS1:-1.23042767295;HOX{A4,D4}:-1.2357901784;NFIL3:-1.38993575948;HIF1A:-1.46997709577;HBP1_HMGB_SSRP1_UBTF:-1.51947610154;NFE2L1:-1.56907895812;PAX8:-1.58174413642;HSF1,2:-1.70396677396;PPARG:-1.85535681249;HES1:-1.93468325105;STAT5{A,B}:-2.15027602139 | ||
|comment= | |comment= | ||
|created_by= | |created_by= | ||
Revision as of 18:06, 14 March 2012
| Name: | small intestine, fetal, donor1 |
|---|---|
| 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: CNhs11773
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: CNhs11773
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.113 |
| 10 | 10 | 0.155 |
| 100 | 100 | 0.601 |
| 101 | 101 | 0.833 |
| 102 | 102 | 0.226 |
| 103 | 103 | 0.809 |
| 104 | 104 | 0.597 |
| 105 | 105 | 0.499 |
| 106 | 106 | 0.391 |
| 107 | 107 | 0.123 |
| 108 | 108 | 0.647 |
| 109 | 109 | 0.0999 |
| 11 | 11 | 0.54 |
| 110 | 110 | 0.419 |
| 111 | 111 | 0.391 |
| 112 | 112 | 0.403 |
| 113 | 113 | 0.0136 |
| 114 | 114 | 0.15 |
| 115 | 115 | 0.557 |
| 116 | 116 | 0.427 |
| 117 | 117 | 0.00723 |
| 118 | 118 | 0.538 |
| 119 | 119 | 0.646 |
| 12 | 12 | 0.796 |
| 120 | 120 | 0.815 |
| 121 | 121 | 0.319 |
| 122 | 122 | 0.56 |
| 123 | 123 | 0.854 |
| 124 | 124 | 0.215 |
| 125 | 125 | 0.346 |
| 126 | 126 | 0.729 |
| 127 | 127 | 0.277 |
| 128 | 128 | 0.0416 |
| 129 | 129 | 0.959 |
| 13 | 13 | 0.304 |
| 130 | 130 | 0.83 |
| 131 | 131 | 0.585 |
| 132 | 132 | 0.0161 |
| 133 | 133 | 0.52 |
| 134 | 134 | 0.827 |
| 135 | 135 | 0.436 |
| 136 | 136 | 0.518 |
| 137 | 137 | 0.108 |
| 138 | 138 | 0.682 |
| 139 | 139 | 0.0456 |
| 14 | 14 | 0.481 |
| 140 | 140 | 0.668 |
| 141 | 141 | 0.544 |
| 142 | 142 | 0.908 |
| 143 | 143 | 0.0103 |
| 144 | 144 | 0.743 |
| 145 | 145 | 0.622 |
| 146 | 146 | 0.373 |
| 147 | 147 | 0.547 |
| 148 | 148 | 0.659 |
| 149 | 149 | 0.208 |
| 15 | 15 | 0.136 |
| 150 | 150 | 0.714 |
| 151 | 151 | 0.805 |
| 152 | 152 | 0.128 |
| 153 | 153 | 0.839 |
| 154 | 154 | 0.758 |
| 155 | 155 | 0.743 |
| 156 | 156 | 0.314 |
| 157 | 157 | 0.773 |
| 158 | 158 | 0.552 |
| 159 | 159 | 0.205 |
| 16 | 16 | 0.763 |
| 160 | 160 | 0.861 |
| 161 | 161 | 0.907 |
| 162 | 162 | 0.201 |
| 163 | 163 | 0.204 |
| 164 | 164 | 0.87 |
| 165 | 165 | 0.855 |
| 166 | 166 | 0.44 |
| 167 | 167 | 0.371 |
| 168 | 168 | 0.678 |
| 169 | 169 | 0.7 |
| 17 | 17 | 0.902 |
| 18 | 18 | 0.00639 |
| 19 | 19 | 0.251 |
| 2 | 2 | 0.0172 |
| 20 | 20 | 0.0923 |
| 21 | 21 | 0.592 |
| 22 | 22 | 0.915 |
| 23 | 23 | 0.964 |
| 24 | 24 | 0.583 |
| 25 | 25 | 0.413 |
| 26 | 26 | 0.737 |
| 27 | 27 | 0.352 |
| 28 | 28 | 0.657 |
| 29 | 29 | 0.12 |
| 3 | 3 | 0.464 |
| 30 | 30 | 0.0527 |
| 31 | 31 | 0.665 |
| 32 | 32 | 0.00595 |
| 33 | 33 | 0.359 |
| 34 | 34 | 0.223 |
| 35 | 35 | 0.233 |
| 36 | 36 | 0.0161 |
| 37 | 37 | 0.115 |
| 38 | 38 | 0.867 |
| 39 | 39 | 0.336 |
| 4 | 4 | 0.482 |
| 40 | 40 | 0.834 |
| 41 | 41 | 0.0195 |
| 42 | 42 | 0.326 |
| 43 | 43 | 0.316 |
| 44 | 44 | 0.0478 |
| 45 | 45 | 0.475 |
| 46 | 46 | 0.384 |
| 47 | 47 | 0.454 |
| 48 | 48 | 0.95 |
| 49 | 49 | 0.0436 |
| 5 | 5 | 0.219 |
| 50 | 50 | 0.591 |
| 51 | 51 | 0.706 |
| 52 | 52 | 0.132 |
| 53 | 53 | 0.595 |
| 54 | 54 | 0.738 |
| 55 | 55 | 0.291 |
| 56 | 56 | 0.962 |
| 57 | 57 | 0.229 |
| 58 | 58 | 0.866 |
| 59 | 59 | 0.559 |
| 6 | 6 | 0.675 |
| 60 | 60 | 0.393 |
| 61 | 61 | 0.345 |
| 62 | 62 | 0.417 |
| 63 | 63 | 0.475 |
| 64 | 64 | 0.957 |
| 65 | 65 | 0.893 |
| 66 | 66 | 0.0101 |
| 67 | 67 | 0.432 |
| 68 | 68 | 0.279 |
| 69 | 69 | 0.706 |
| 7 | 7 | 0.552 |
| 70 | 70 | 0.248 |
| 71 | 71 | 0.071 |
| 72 | 72 | 0.451 |
| 73 | 73 | 0.478 |
| 74 | 74 | 0.0711 |
| 75 | 75 | 0.00534 |
| 76 | 76 | 0.162 |
| 77 | 77 | 0.132 |
| 78 | 78 | 0.45 |
| 79 | 79 | 0.238 |
| 8 | 8 | 0.456 |
| 80 | 80 | 0.807 |
| 81 | 81 | 0.291 |
| 82 | 82 | 0.742 |
| 83 | 83 | 0.724 |
| 84 | 84 | 0.99 |
| 85 | 85 | 0.747 |
| 86 | 86 | 0.148 |
| 87 | 87 | 0.0515 |
| 88 | 88 | 0.85 |
| 89 | 89 | 0.91 |
| 9 | 9 | 0.842 |
| 90 | 90 | 0.062 |
| 91 | 91 | 0.66 |
| 92 | 92 | 0.901 |
| 93 | 93 | 0.104 |
| 94 | 94 | 0.0368 |
| 95 | 95 | 0.19 |
| 96 | 96 | 0.411 |
| 97 | 97 | 0.152 |
| 98 | 98 | 0.409 |
| 99 | 99 | 0.0482 |
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: CNhs11773
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000004 tissue sample
FF:0000210 human sample
FF:0010064 human small intestine - fetal 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
UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000160 (intestine)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002108 (small intestine)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)
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
