FF:10209-103G2: Difference between revisions
From FANTOM5_SSTAR
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}:5.61196180699;NR1H4:3.96404242888;TBP:3.7962538106;NR5A1,2:3.28126490671;TBX4,5:2.86280608259;MYOD1:2.84009449375;TFCP2:2.72264858926;ESR1:2.65812466028;NFE2L1:2.56703412453;HMX1:2.54883574426;TAL1_TCF{3,4,12}:2.50799343005;RXRA_VDR{dimer}:2.33600033877;TLX2:2.31562146086;RXR{A,B,G}_{NR1H2,PPAR}dimers:2.26102509303;TGIF1:2.1930115062;SNAI1..3:2.18957137949;TFAP2{A,C}:2.10926322123;TFAP4:2.10370630453;LMO2:2.08932543912;HAND1,2:2.04620125224;ESRRA:1.95584912042;GLI1..3:1.80931942402;SPZ1:1.80147771441;SRF:1.78623230924;TLX1..3_NFIC{dimer}:1.78035407765;NR6A1:1.76145061219;ZEB1:1.73516845693;SMAD1..7,9:1.71767936149;GCM1,2:1.70999634925;RBPJ:1.64272150846;MAZ:1.63223461973;FOXO1,3,4:1.61675297774;FOXL1:1.59841160708;ZIC1..3:1.58871034931;ZNF148:1.57623217605;AR:1.51613125847;SP1:1.49074892653;NHLH1,2:1.43170050136;PDX1:1.42700844051;HOX{A4,D4}:1.42374584659;SOX5:1.38128459689;RFX2..5_RFXANK_RFXAP:1.36298693989;PAX6:1.32987745865;IRF7:1.26819340116;MYFfamily:1.22285547815;PATZ1:1.22079414847;KLF4:1.2185733849;MAFB:1.17623070794;MYBL2:1.16268079286;ZNF423:1.15843810524;MTF1:1.13279430153;FOX{D1,D2}:1.12017998003;NFATC1..3:1.0889251308;GATA4:1.08435806295;HIC1:1.08307177142;T:1.07585362086;GTF2A1,2:1.06929396392;NKX2-2,8:1.02287284555;RREB1:0.980064876786;NFIX:0.972760135995;ZNF384:0.937080348026;ATF2:0.902737267147;PPARG:0.865467502179;GTF2I:0.856499222402;TP53:0.853238074234;NKX6-1,2:0.780701797713;BPTF:0.752540004186;ZNF238:0.75097613257;TEAD1:0.741281271173;IKZF2:0.732084399857;ATF6:0.728367465419;FOX{F1,F2,J1}:0.715453116023;HES1:0.711964508576;FOXA2:0.693917357743;HSF1,2:0.674232619786;FOXN1:0.668005246931;UFEwm:0.650014169425;NKX3-2:0.648794970108;MED-1{core}:0.645292236866;XCPE1{core}:0.615359548554;PAX5:0.594099197192;XBP1:0.580444743003;CUX2:0.539030185726;MZF1:0.538059692689;NKX2-3_NKX2-5:0.535618702664;POU6F1:0.526745612448;ALX1:0.509456148996;EP300:0.508977836827;ALX4:0.467487903149;RXR{A,B,G}:0.465975855766;YY1:0.46596276337;NANOG:0.401403404918;REST:0.40114374;EBF1:0.385396216669;MTE{core}:0.380226898107;GATA6:0.379274330416;TFAP2B:0.372803823707;ETS1,2:0.355683348095;RFX1:0.339068793515;IKZF1:0.300051732283;CDC5L:0.278118194807;ARID5B:0.263967235278;POU2F1..3:0.254954071782;EVI1:0.186782783296;POU5F1:0.175259293733;PITX1..3:0.164729773223;PAX1,9:0.146414541416;PBX1:0.146349368171;EGR1..3:0.104746118632;JUN:0.0832958308451;IRF1,2:0.0645077977105;HNF4A_NR2F1,2:0.0607134404148;SOX{8,9,10}:0.0556137766978;FOXQ1:0.0484390902421;HBP1_HMGB_SSRP1_UBTF:0.0454143653537;GFI1B:0.0350801980635;ELF1,2,4:0.0334135408275;STAT5{A,B}:0.0328965524019;DMAP1_NCOR{1,2}_SMARC:0.0175184562831;SPI1:0.0137244080886;POU3F1..4:-0.00230503336224;ATF4:-0.042753527621;PRDM1:-0.0431704842127;CDX1,2,4:-0.0436305951378;ZFP161:-0.051886519546;FOXP1:-0.0605995041719;SREBF1,2:-0.0713741267115;BREu{core}:-0.0842191218801;NR3C1:-0.088720111794;STAT2,4,6:-0.0989056898655;CEBPA,B_DDIT3:-0.108247837143;ZNF143:-0.123842677557;SPIB:-0.126483237775;LEF1_TCF7_TCF7L1,2:-0.154839364061;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.157322148287;GFI1:-0.179046147143;STAT1,3:-0.188191435788;EN1,2:-0.199398992816;NFE2L2:-0.21081965604;POU1F1:-0.217296449432;FOSL2:-0.227724355285;FOXM1:-0.228877191976;ZBTB6:-0.247151791775;NKX2-1,4:-0.293630275924;NFY{A,B,C}:-0.299023705942;TOPORS:-0.334712631348;PAX3,7:-0.377526326881;NFIL3:-0.418428709331;NFE2:-0.418992112021;PAX2:-0.423861936178;LHX3,4:-0.444452487613;FOXP3:-0.457761420478;SOX17:-0.48258330601;ATF5_CREB3:-0.502076143428;NFKB1_REL_RELA:-0.525840554635;FOS_FOS{B,L1}_JUN{B,D}:-0.525867686029;RUNX1..3:-0.53742729271;SOX2:-0.569798789477;E2F1..5:-0.582414761521;HLF:-0.631778215635;ZBTB16:-0.63235240239;HNF1A:-0.63677402647;NANOG{mouse}:-0.678474987927;GZF1:-0.722583748313;NRF1:-0.724758427118;bHLH_family:-0.799177295818;BACH2:-0.819656796534;AIRE:-0.824484164744;NKX3-1:-0.885108538871;CREB1:-0.91959773943;RORA:-0.934143958107;HOX{A6,A7,B6,B7}:-0.937979666827;OCT4_SOX2{dimer}:-0.961344324723;VSX1,2:-1.09474625664;TEF:-1.16644783584;CRX:-1.17019351543;TFDP1:-1.27950503847;HMGA1,2:-1.29665469638;DBP:-1.29997547187;ONECUT1,2:-1.3488522013;MYB:-1.38599907877;HIF1A:-1.45520774942;FOX{I1,J2}:-1.48106638637;ELK1,4_GABP{A,B1}:-1.49762547859;HOX{A5,B5}:-1.51611493142;AHR_ARNT_ARNT2:-1.66244304754;PAX4:-1.68873363185;PRRX1,2:-1.72881840546;HOXA9_MEIS1:-1.73385942474;FOXD3:-1.85081081981;ADNP_IRX_SIX_ZHX:-1.92391232388;PAX8:-3.18167568425 | ||
|comment= | |comment= | ||
|created_by= | |created_by= |
Revision as of 18:07, 14 March 2012
Name: | throat, adult |
---|---|
Species: | Human (Homo sapiens) |
Library ID: | {{{library_id}}} |
Sample type: | {{{sample_category}}} |
Genomic View: | UCSC |
CAGEd-oPOSSUM: | link |
Additional information | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample information
RNA information
|
Download raw sequence, BAM & CTSS | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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: CNhs12858
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: CNhs12858
Novel motif | Logo | P-value |
---|---|---|
1 | 1 | 0.811 |
10 | 10 | 0.106 |
100 | 100 | 0.329 |
101 | 101 | 0.111 |
102 | 102 | 0.833 |
103 | 103 | 0.4 |
104 | 104 | 0.713 |
105 | 105 | 0.718 |
106 | 106 | 0.423 |
107 | 107 | 0.0831 |
108 | 108 | 0.218 |
109 | 109 | 0.828 |
11 | 11 | 0.84 |
110 | 110 | 0.689 |
111 | 111 | 0.46 |
112 | 112 | 0.0793 |
113 | 113 | 0.898 |
114 | 114 | 0.171 |
115 | 115 | 0.0627 |
116 | 116 | 0.468 |
117 | 117 | 0.192 |
118 | 118 | 0.0296 |
119 | 119 | 0.282 |
12 | 12 | 0.774 |
120 | 120 | 0.716 |
121 | 121 | 0.518 |
122 | 122 | 0.391 |
123 | 123 | 0.019 |
124 | 124 | 0.323 |
125 | 125 | 0.828 |
126 | 126 | 0.138 |
127 | 127 | 0.758 |
128 | 128 | 0.189 |
129 | 129 | 0.368 |
13 | 13 | 0.375 |
130 | 130 | 0.745 |
131 | 131 | 0.408 |
132 | 132 | 0.043 |
133 | 133 | 1.0711e-4 |
134 | 134 | 0.0048 |
135 | 135 | 0.0636 |
136 | 136 | 0.654 |
137 | 137 | 0.326 |
138 | 138 | 0.512 |
139 | 139 | 0.419 |
14 | 14 | 0.505 |
140 | 140 | 0.888 |
141 | 141 | 0.964 |
142 | 142 | 0.567 |
143 | 143 | 0.00506 |
144 | 144 | 0.671 |
145 | 145 | 0.952 |
146 | 146 | 0.686 |
147 | 147 | 0.0203 |
148 | 148 | 0.906 |
149 | 149 | 0.0124 |
15 | 15 | 0.368 |
150 | 150 | 0.884 |
151 | 151 | 0.406 |
152 | 152 | 0.102 |
153 | 153 | 0.485 |
154 | 154 | 0.64 |
155 | 155 | 0.611 |
156 | 156 | 0.111 |
157 | 157 | 0.907 |
158 | 158 | 0.0762 |
159 | 159 | 0.841 |
16 | 16 | 0.346 |
160 | 160 | 0.705 |
161 | 161 | 0.692 |
162 | 162 | 0.503 |
163 | 163 | 0.106 |
164 | 164 | 0.197 |
165 | 165 | 0.0359 |
166 | 166 | 0.0884 |
167 | 167 | 0.0614 |
168 | 168 | 0.144 |
169 | 169 | 0.0481 |
17 | 17 | 0.879 |
18 | 18 | 0.0812 |
19 | 19 | 0.126 |
2 | 2 | 0.00823 |
20 | 20 | 0.0546 |
21 | 21 | 0.643 |
22 | 22 | 0.139 |
23 | 23 | 0.331 |
24 | 24 | 0.567 |
25 | 25 | 0.835 |
26 | 26 | 0.536 |
27 | 27 | 0.398 |
28 | 28 | 0.974 |
29 | 29 | 0.184 |
3 | 3 | 0.78 |
30 | 30 | 0.00751 |
31 | 31 | 0.766 |
32 | 32 | 0.226 |
33 | 33 | 0.506 |
34 | 34 | 0.278 |
35 | 35 | 0.597 |
36 | 36 | 0.0126 |
37 | 37 | 0.941 |
38 | 38 | 0.779 |
39 | 39 | 0.199 |
4 | 4 | 0.655 |
40 | 40 | 0.234 |
41 | 41 | 0.481 |
42 | 42 | 0.461 |
43 | 43 | 0.672 |
44 | 44 | 0.0312 |
45 | 45 | 0.027 |
46 | 46 | 0.84 |
47 | 47 | 0.571 |
48 | 48 | 0.579 |
49 | 49 | 0.435 |
5 | 5 | 0.644 |
50 | 50 | 0.387 |
51 | 51 | 0.703 |
52 | 52 | 0.069 |
53 | 53 | 0.683 |
54 | 54 | 0.924 |
55 | 55 | 0.978 |
56 | 56 | 0.889 |
57 | 57 | 0.383 |
58 | 58 | 0.966 |
59 | 59 | 0.16 |
6 | 6 | 0.728 |
60 | 60 | 0.211 |
61 | 61 | 0.612 |
62 | 62 | 0.805 |
63 | 63 | 0.324 |
64 | 64 | 0.827 |
65 | 65 | 0.479 |
66 | 66 | 0.00837 |
67 | 67 | 0.241 |
68 | 68 | 0.23 |
69 | 69 | 0.379 |
7 | 7 | 0.682 |
70 | 70 | 0.665 |
71 | 71 | 0.363 |
72 | 72 | 0.637 |
73 | 73 | 0.573 |
74 | 74 | 0.126 |
75 | 75 | 0.301 |
76 | 76 | 0.0105 |
77 | 77 | 0.0105 |
78 | 78 | 0.906 |
79 | 79 | 0.472 |
8 | 8 | 0.931 |
80 | 80 | 0.638 |
81 | 81 | 0.696 |
82 | 82 | 0.417 |
83 | 83 | 0.719 |
84 | 84 | 0.906 |
85 | 85 | 0.112 |
86 | 86 | 0.714 |
87 | 87 | 0.847 |
88 | 88 | 0.63 |
89 | 89 | 0.0956 |
9 | 9 | 0.459 |
90 | 90 | 0.0659 |
91 | 91 | 0.0976 |
92 | 92 | 0.407 |
93 | 93 | 0.95 |
94 | 94 | 0.0791 |
95 | 95 | 0.395 |
96 | 96 | 0.64 |
97 | 97 | 0.813 |
98 | 98 | 0.999 |
99 | 99 | 0.112 |
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: CNhs12858
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000004 tissue sample
FF:0000210 human sample
FF:0010209 human throat - adult 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)
0000341 (throat)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0001062 (anatomical entity)
0007023 (adult organism)
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