FF:10772-110F7: Difference between revisions
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|top_motifs= | |top_motifs=MYB:2.12624025534;E2F1..5:1.75324808807;NFY{A,B,C}:1.33489119083;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.21022376933;bHLH_family:1.13279903785;YY1:1.06653108576;EP300:1.05569388078;ELK1,4_GABP{A,B1}:0.953035414514;BREu{core}:0.945066593907;NRF1:0.936691468057;HBP1_HMGB_SSRP1_UBTF:0.906302498831;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.891038838446;SPIB:0.859059981313;ELF1,2,4:0.857523098169;HIF1A:0.823036870189;ZNF143:0.807474864577;TEF:0.805602661482;SPI1:0.725748955664;PAX8:0.720399714416;PITX1..3:0.710945131674;FOXP1:0.708416259787;DMAP1_NCOR{1,2}_SMARC:0.697543621606;POU5F1:0.654171802531;RUNX1..3:0.62899880336;NANOG{mouse}:0.59009013131;NANOG:0.587599189126;MYOD1:0.553150462497;FOXA2:0.523702872002;VSX1,2:0.51521243888;NKX2-2,8:0.503642181705;NR5A1,2:0.491609171838;ETS1,2:0.425378685853;NKX3-1:0.407238499901;TLX2:0.385698222515;CEBPA,B_DDIT3:0.372622048165;NR6A1:0.367192622365;POU2F1..3:0.354693767216;PBX1:0.34769536293;FOXQ1:0.294835965378;POU3F1..4:0.288452662781;TFDP1:0.286518365425;GATA6:0.281166829808;NFIL3:0.268763932995;CRX:0.256104428371;RFX2..5_RFXANK_RFXAP:0.237839734555;GFI1:0.219484906947;OCT4_SOX2{dimer}:0.202747472133;RBPJ:0.200835448283;CUX2:0.198071036394;HOX{A6,A7,B6,B7}:0.188677185404;FOXD3:0.169794191914;POU1F1:0.168950293125;PAX4:0.164824070734;FOXP3:0.146018900838;PAX5:0.144131290864;HAND1,2:0.14227786506;DBP:0.0983103862964;ZNF238:0.094355380958;TOPORS:0.093388437846;SOX{8,9,10}:0.0864377217255;MTF1:0.0734435365819;ONECUT1,2:0.061832007506;IRF7:0.0597757023907;HOXA9_MEIS1:0.0462277377229;AHR_ARNT_ARNT2:0.0391719458656;NKX2-3_NKX2-5:0.0259282557579;AIRE:0.0166023573604;PDX1:0.0158545787439;HLF:-0.00368067901915;PRRX1,2:-0.00402001736586;ATF5_CREB3:-0.00592425028821;ALX1:-0.00858037462466;IRF1,2:-0.0255094123408;ARID5B:-0.0516649899989;PAX2:-0.0528110943743;REST:-0.0567300090631;CDX1,2,4:-0.0684361361346;AR:-0.0801437482117;BPTF:-0.0813257165345;STAT1,3:-0.0852808793551;EN1,2:-0.0872851547187;IKZF1:-0.0993325194871;LHX3,4:-0.101900806663;HOX{A4,D4}:-0.109315083936;ZNF423:-0.121975672243;HNF1A:-0.146391586424;SNAI1..3:-0.157650242084;PAX6:-0.173935016684;FOXM1:-0.18057553789;ZEB1:-0.184253202001;NKX2-1,4:-0.195591793986;PRDM1:-0.199856303762;HOX{A5,B5}:-0.214047903448;GCM1,2:-0.21743472348;MEF2{A,B,C,D}:-0.225681821917;NKX6-1,2:-0.265557577685;ATF4:-0.266274311597;SREBF1,2:-0.274133640816;FOX{I1,J2}:-0.276667457066;ZBTB16:-0.279170585272;HNF4A_NR2F1,2:-0.281821581435;TBP:-0.285833022075;CREB1:-0.315522223076;PAX3,7:-0.318961046535;IKZF2:-0.32686001174;RFX1:-0.33381017432;KLF4:-0.339540103526;NHLH1,2:-0.369183756759;POU6F1:-0.375598552275;ZFP161:-0.376727130712;NFKB1_REL_RELA:-0.377668241048;MZF1:-0.396248060271;FOX{F1,F2,J1}:-0.428833070205;MYBL2:-0.436745829896;EBF1:-0.448505887404;FOXN1:-0.492744382888;SP1:-0.494073583656;FOS_FOS{B,L1}_JUN{B,D}:-0.495629814988;TGIF1:-0.50151455551;STAT5{A,B}:-0.503516977125;NFE2:-0.510605060022;GATA4:-0.511301438835;RORA:-0.51219162525;HSF1,2:-0.517009157769;FOSL2:-0.517522136314;HES1:-0.517898992445;BACH2:-0.586536035042;UFEwm:-0.597445328423;HIC1:-0.600679103732;LMO2:-0.604367155018;MYFfamily:-0.615287400212;ESRRA:-0.621020668459;ZNF384:-0.637481830736;TFAP2B:-0.64274476932;LEF1_TCF7_TCF7L1,2:-0.65670991321;ALX4:-0.657344607364;SOX17:-0.657703680293;ADNP_IRX_SIX_ZHX:-0.666740043789;PPARG:-0.677918895494;NFIX:-0.70977176692;NKX3-2:-0.71141937957;XBP1:-0.712942742295;SOX5:-0.763281963561;NFE2L2:-0.782637124075;T:-0.783483689804;GTF2A1,2:-0.802434056168;GTF2I:-0.816613769554;ZNF148:-0.822158957924;TP53:-0.851525798993;ATF2:-0.858487429773;ATF6:-0.864179314951;ESR1:-0.877262514368;EVI1:-0.881862114929;GZF1:-0.912408757234;MTE{core}:-0.92086415089;NR3C1:-0.928347183336;RREB1:-0.934575147945;MED-1{core}:-0.956489243866;NFE2L1:-0.976837710407;FOX{D1,D2}:-0.98401615716;FOXL1:-0.986286389159;STAT2,4,6:-0.992187144066;RXRA_VDR{dimer}:-0.994530807788;NR1H4:-0.999540003067;TFAP2{A,C}:-1.00293971155;FOXO1,3,4:-1.00608115397;SRF:-1.01687067241;ZIC1..3:-1.01714050609;TEAD1:-1.03791213683;XCPE1{core}:-1.04341144588;PATZ1:-1.04899156582;MAFB:-1.12335408241;TLX1..3_NFIC{dimer}:-1.12910460208;SOX2:-1.16223171981;HMGA1,2:-1.17114692759;TAL1_TCF{3,4,12}:-1.17284027015;MAZ:-1.18427185311;TFAP4:-1.2226421821;ZBTB6:-1.2306375551;RXR{A,B,G}:-1.24282110954;EGR1..3:-1.24473999066;GFI1B:-1.30083365055;PAX1,9:-1.32553013507;CDC5L:-1.36499331047;SMAD1..7,9:-1.38427945786;TFCP2:-1.42652040703;SPZ1:-1.46998970392;HMX1:-1.49533187031;JUN:-1.51322175239;NFATC1..3:-1.53330777443;TBX4,5:-1.63661162985;GLI1..3:-1.7244774484 | ||
|comment= | |comment= | ||
|created_by= | |created_by= |
Revision as of 18:02, 14 March 2012
Name: | myelodysplastic syndrome cell line:SKM-1 |
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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: CNhs11934
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: CNhs11934
Novel motif | Logo | P-value |
---|---|---|
1 | 1 | 0.231 |
10 | 10 | 0.0701 |
100 | 100 | 0.0925 |
101 | 101 | 0.43 |
102 | 102 | 0.694 |
103 | 103 | 0.695 |
104 | 104 | 0.9 |
105 | 105 | 0.903 |
106 | 106 | 0.00122 |
107 | 107 | 0.0457 |
108 | 108 | 0.43 |
109 | 109 | 0.628 |
11 | 11 | 0.257 |
110 | 110 | 0.881 |
111 | 111 | 0.356 |
112 | 112 | 0.741 |
113 | 113 | 0.215 |
114 | 114 | 0.87 |
115 | 115 | 0.745 |
116 | 116 | 0.722 |
117 | 117 | 0.168 |
118 | 118 | 0.308 |
119 | 119 | 0.186 |
12 | 12 | 0.386 |
120 | 120 | 0.622 |
121 | 121 | 0.559 |
122 | 122 | 0.707 |
123 | 123 | 0.191 |
124 | 124 | 0.79 |
125 | 125 | 0.509 |
126 | 126 | 0.577 |
127 | 127 | 0.15 |
128 | 128 | 0.0635 |
129 | 129 | 0.55 |
13 | 13 | 0.00224 |
130 | 130 | 0.445 |
131 | 131 | 0.0404 |
132 | 132 | 0.704 |
133 | 133 | 0.963 |
134 | 134 | 0.435 |
135 | 135 | 0.139 |
136 | 136 | 0.117 |
137 | 137 | 0.781 |
138 | 138 | 0.504 |
139 | 139 | 0.31 |
14 | 14 | 0.582 |
140 | 140 | 0.305 |
141 | 141 | 0.658 |
142 | 142 | 0.251 |
143 | 143 | 0.0767 |
144 | 144 | 0.541 |
145 | 145 | 0.496 |
146 | 146 | 0.648 |
147 | 147 | 0.0634 |
148 | 148 | 0.251 |
149 | 149 | 0.0303 |
15 | 15 | 0.89 |
150 | 150 | 0.513 |
151 | 151 | 0.182 |
152 | 152 | 0.0109 |
153 | 153 | 0.483 |
154 | 154 | 0.734 |
155 | 155 | 0.231 |
156 | 156 | 0.788 |
157 | 157 | 0.0872 |
158 | 158 | 0.326 |
159 | 159 | 0.818 |
16 | 16 | 0.433 |
160 | 160 | 0.706 |
161 | 161 | 0.819 |
162 | 162 | 0.909 |
163 | 163 | 0.52 |
164 | 164 | 0.0574 |
165 | 165 | 0.866 |
166 | 166 | 0.774 |
167 | 167 | 0.535 |
168 | 168 | 0.0645 |
169 | 169 | 0.281 |
17 | 17 | 0.336 |
18 | 18 | 0.212 |
19 | 19 | 0.567 |
2 | 2 | 0.0778 |
20 | 20 | 0.0575 |
21 | 21 | 0.814 |
22 | 22 | 0.248 |
23 | 23 | 0.00391 |
24 | 24 | 0.0782 |
25 | 25 | 0.474 |
26 | 26 | 0.167 |
27 | 27 | 0.713 |
28 | 28 | 0.848 |
29 | 29 | 0.325 |
3 | 3 | 0.447 |
30 | 30 | 0.0844 |
31 | 31 | 0.0954 |
32 | 32 | 0.133 |
33 | 33 | 0.351 |
34 | 34 | 0.712 |
35 | 35 | 0.732 |
36 | 36 | 0.0409 |
37 | 37 | 0.952 |
38 | 38 | 0.846 |
39 | 39 | 0.362 |
4 | 4 | 0.791 |
40 | 40 | 0.151 |
41 | 41 | 0.413 |
42 | 42 | 0.364 |
43 | 43 | 0.466 |
44 | 44 | 0.705 |
45 | 45 | 0.134 |
46 | 46 | 0.973 |
47 | 47 | 0.179 |
48 | 48 | 0.119 |
49 | 49 | 0.642 |
5 | 5 | 0.361 |
50 | 50 | 0.936 |
51 | 51 | 0.648 |
52 | 52 | 0.0267 |
53 | 53 | 0.846 |
54 | 54 | 0.424 |
55 | 55 | 0.197 |
56 | 56 | 0.573 |
57 | 57 | 0.657 |
58 | 58 | 0.48 |
59 | 59 | 0.711 |
6 | 6 | 0.508 |
60 | 60 | 0.0581 |
61 | 61 | 0.331 |
62 | 62 | 0.874 |
63 | 63 | 0.963 |
64 | 64 | 0.457 |
65 | 65 | 0.279 |
66 | 66 | 0.162 |
67 | 67 | 0.942 |
68 | 68 | 0.296 |
69 | 69 | 0.646 |
7 | 7 | 0.303 |
70 | 70 | 0.0381 |
71 | 71 | 0.207 |
72 | 72 | 0.59 |
73 | 73 | 0.198 |
74 | 74 | 0.173 |
75 | 75 | 0.115 |
76 | 76 | 0.276 |
77 | 77 | 0.216 |
78 | 78 | 0.188 |
79 | 79 | 0.0671 |
8 | 8 | 0.488 |
80 | 80 | 0.26 |
81 | 81 | 0.688 |
82 | 82 | 0.194 |
83 | 83 | 0.674 |
84 | 84 | 0.757 |
85 | 85 | 0.00156 |
86 | 86 | 0.686 |
87 | 87 | 0.187 |
88 | 88 | 0.407 |
89 | 89 | 0.216 |
9 | 9 | 0.999 |
90 | 90 | 0.278 |
91 | 91 | 0.0978 |
92 | 92 | 0.0358 |
93 | 93 | 0.904 |
94 | 94 | 0.915 |
95 | 95 | 0.407 |
96 | 96 | 0.469 |
97 | 97 | 0.383 |
98 | 98 | 0.878 |
99 | 99 | 0.678 |
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: CNhs11934
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
DOID:225 syndrome
DOID:74 hematopoietic system disease
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human 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
DOID: Disease
1287 (cardiovascular system disease)
225 (syndrome)
4 (disease)
7 (disease of anatomical entity)
74 (hematopoietic system 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