FF:10787-110H4: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |F5samples= | ||
| | |ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384 | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
|ancestors_in_disease_facet=DOID:0050687,DOID:1115,DOID:14566,DOID:162,DOID:4 | |ancestors_in_disease_facet=DOID:0050687,DOID:1115,DOID:14566,DOID:162,DOID:4 | ||
| | |comment= | ||
|created_by= | |||
|creation_date= | |||
|def= | |||
|fonse_cell_line=FF:0100400 | |fonse_cell_line=FF:0100400 | ||
|fonse_cell_line_closure=FF:0100400 | |fonse_cell_line_closure=FF:0100400 | ||
Line 66: | Line 34: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|id=FF:10787-110H4 | |||
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102267 | |is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102267 | ||
|name=rhabdomyosarcoma cell line:KYM-1 | |||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
|profile_cagescan=,,, | |||
|profile_hcage=CNhs11877,LSID830,release010,COMPLETED | |||
|profile_rnaseq=,,, | |||
|profile_srnaseq=,,, | |||
|rna_box=110 | |||
|rna_catalog_number= | |||
|rna_concentration=1.33674 | |||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |||
|rna_lot_number= | |||
|rna_od260/230=2.13 | |||
|rna_od260/280=2.05 | |||
|rna_position=H4 | |||
|rna_rin= | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=110H4 | |||
|rna_weight_ug=36.09198 | |||
|sample_age=9 months | |||
|sample_cell_catalog=jcrb0627 | |||
|sample_cell_line=KYM-1 | |||
|sample_cell_lot= | |||
|sample_cell_type=unclassifiable | |||
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest) | |||
|sample_company=JAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank | |||
|sample_description= | |||
|sample_dev_stage= | |||
|sample_disease=rhabdomyosarcoma | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity=J | |||
|sample_experimental_condition= | |||
|sample_id=10787 | |||
|sample_note= | |||
|sample_sex=female | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue=neck | |||
|top_motifs=VSX1,2:2.88606492891;PDX1:2.80725612372;POU1F1:2.21156246466;NKX2-1,4:2.0746203796;PBX1:1.9818727196;PITX1..3:1.91727403365;RORA:1.86730468971;PAX4:1.8596927012;PAX8:1.80164552664;NRF1:1.63137160693;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.59019033304;HOX{A4,D4}:1.58860315789;POU3F1..4:1.55775628757;E2F1..5:1.46040508349;EN1,2:1.41088012344;NFY{A,B,C}:1.40100275321;IKZF2:1.39029573507;CDX1,2,4:1.36568331751;TOPORS:1.36176933494;ONECUT1,2:1.31944772463;HOX{A5,B5}:1.31348423062;YY1:1.31149386191;FOXP1:1.27178832496;FOXD3:1.24234449868;RFX1:1.19097483503;HOX{A6,A7,B6,B7}:1.15054853896;GFI1:1.13244695363;ZNF384:1.12553807584;PRRX1,2:1.1078293894;AIRE:1.07190481802;ZNF143:1.02581482176;ZBTB16:1.02397558631;RFX2..5_RFXANK_RFXAP:1.02093277679;DBP:1.00879205062;FOXQ1:0.999579405582;ELK1,4_GABP{A,B1}:0.996812496271;FOXA2:0.946123046698;TEF:0.927238223593;NKX2-3_NKX2-5:0.920528487354;SOX{8,9,10}:0.892069456105;POU2F1..3:0.878170029641;MYB:0.876877261323;CUX2:0.848422551774;LEF1_TCF7_TCF7L1,2:0.771867883883;CDC5L:0.757145124636;FOXP3:0.752004206979;CRX:0.740947668625;ALX1:0.725916710098;HOXA9_MEIS1:0.722747222933;ADNP_IRX_SIX_ZHX:0.705946940363;ARID5B:0.695709306842;PAX3,7:0.684685754663;ZIC1..3:0.659461604887;MZF1:0.619816914236;NR5A1,2:0.552035759972;ZBTB6:0.53405085956;AHR_ARNT_ARNT2:0.514868089181;OCT4_SOX2{dimer}:0.509618307888;STAT5{A,B}:0.505965696181;RXR{A,B,G}:0.466653863921;GTF2A1,2:0.459943611339;NR3C1:0.450820602865;EVI1:0.445113327516;RXRA_VDR{dimer}:0.440157595818;RBPJ:0.361282640381;BREu{core}:0.353775729589;TGIF1:0.344081105023;NKX3-1:0.342814736505;HIF1A:0.339291795818;SOX17:0.338556978774;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.323288643928;HSF1,2:0.279097115927;PATZ1:0.240248804942;IKZF1:0.200151285677;POU5F1:0.168594434879;GFI1B:0.134719449644;POU6F1:0.133809849222;LHX3,4:0.125592443197;HMGA1,2:0.116896085084;DMAP1_NCOR{1,2}_SMARC:0.112475074731;HAND1,2:0.108636735168;CREB1:0.105132546791;NKX3-2:0.0968220585123;ZEB1:0.0900486374116;SNAI1..3:0.0357135138051;HNF4A_NR2F1,2:0.0330031063993;NKX6-1,2:0.0155705216034;FOXM1:-0.000957755540653;NANOG:-0.0123550215041;T:-0.0192207202919;TLX1..3_NFIC{dimer}:-0.0383922412789;NR6A1:-0.0396779571978;TFDP1:-0.0413500516363;GATA6:-0.04799521336;PAX1,9:-0.0593031527182;HNF1A:-0.0918613850144;PPARG:-0.094693120996;AR:-0.106454028834;UFEwm:-0.137714214717;FOXL1:-0.177972386139;KLF4:-0.186727990124;RUNX1..3:-0.20338476031;HIC1:-0.217771972888;EGR1..3:-0.230502219907;TP53:-0.246726598007;ATF5_CREB3:-0.252556778831;ZFP161:-0.316285882138;TLX2:-0.319004707646;GTF2I:-0.323697031949;XCPE1{core}:-0.330957549572;MEF2{A,B,C,D}:-0.338042425889;EBF1:-0.346637447965;REST:-0.368315258072;SREBF1,2:-0.371084992149;NFKB1_REL_RELA:-0.380214069679;NFE2L2:-0.380888299632;TEAD1:-0.396060757181;SPIB:-0.401851717528;ATF4:-0.40551564578;FOSL2:-0.410494472113;NKX2-2,8:-0.423351971355;BACH2:-0.425335594971;MYBL2:-0.426380693042;NHLH1,2:-0.438046646233;FOX{I1,J2}:-0.459180923898;STAT1,3:-0.492931867323;HBP1_HMGB_SSRP1_UBTF:-0.517116643722;IRF7:-0.518852236512;IRF1,2:-0.533534636314;ALX4:-0.548414406469;GATA4:-0.560774270857;PAX6:-0.569507336921;FOS_FOS{B,L1}_JUN{B,D}:-0.570758926284;JUN:-0.57641537679;MED-1{core}:-0.577486101992;ELF1,2,4:-0.579143932235;FOX{D1,D2}:-0.581660775893;MTF1:-0.587142102087;SOX5:-0.613474253004;NANOG{mouse}:-0.63702453906;TBP:-0.64073899907;STAT2,4,6:-0.641384647526;MYFfamily:-0.647526999687;FOXN1:-0.66216469701;bHLH_family:-0.693615183681;PRDM1:-0.710688863146;SPI1:-0.727644283583;LMO2:-0.728347037916;PAX5:-0.74118879731;NFIX:-0.761879167817;RREB1:-0.771992611143;HLF:-0.776695592743;ZNF148:-0.784695719242;SOX2:-0.797297767917;TAL1_TCF{3,4,12}:-0.79890749103;HES1:-0.806441747972;TFAP2{A,C}:-0.807490461684;NFIL3:-0.81253617614;SPZ1:-0.820918091057;MAZ:-0.83756137323;ATF6:-0.852297203906;CEBPA,B_DDIT3:-0.864398128411;XBP1:-0.87180287944;NFE2:-0.871916634494;ETS1,2:-0.877271794197;ESRRA:-0.889472205244;SMAD1..7,9:-0.890864152101;SP1:-0.911271345786;SRF:-0.918251025385;GCM1,2:-0.928441482301;FOXO1,3,4:-0.951451078113;GLI1..3:-0.976242879087;ZNF238:-1.02630449057;FOX{F1,F2,J1}:-1.02792376188;ATF2:-1.04983633333;ZNF423:-1.05701567139;HMX1:-1.07089630244;PAX2:-1.08165772039;MYOD1:-1.14755228748;TFAP2B:-1.15105518994;BPTF:-1.15453526341;EP300:-1.17302214897;NR1H4:-1.22469461857;ESR1:-1.2310461728;NFE2L1:-1.27882824428;GZF1:-1.27890411681;MTE{core}:-1.35391004757;MAFB:-1.40138600637;NFATC1..3:-1.48611190746;TFCP2:-1.54437788314;TBX4,5:-1.59178616813;TFAP4:-1.86052145023 | |||
}} | }} |
Revision as of 14:15, 21 March 2012
Name: | rhabdomyosarcoma cell line:KYM-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: CNhs11877
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: CNhs11877
Novel motif | Logo | P-value |
---|---|---|
1 | 1 | 0.665 |
10 | 10 | 0.467 |
100 | 100 | 0.261 |
101 | 101 | 0.994 |
102 | 102 | 0.993 |
103 | 103 | 0.168 |
104 | 104 | 0.683 |
105 | 105 | 0.577 |
106 | 106 | 1.03178e-4 |
107 | 107 | 0.0302 |
108 | 108 | 0.262 |
109 | 109 | 0.897 |
11 | 11 | 0.768 |
110 | 110 | 0.326 |
111 | 111 | 0.847 |
112 | 112 | 0.164 |
113 | 113 | 0.0774 |
114 | 114 | 0.381 |
115 | 115 | 0.596 |
116 | 116 | 0.442 |
117 | 117 | 0.0612 |
118 | 118 | 0.465 |
119 | 119 | 0.681 |
12 | 12 | 0.344 |
120 | 120 | 0.815 |
121 | 121 | 0.215 |
122 | 122 | 0.286 |
123 | 123 | 0.0301 |
124 | 124 | 0.627 |
125 | 125 | 0.488 |
126 | 126 | 0.862 |
127 | 127 | 0.216 |
128 | 128 | 0.122 |
129 | 129 | 0.117 |
13 | 13 | 0.398 |
130 | 130 | 0.652 |
131 | 131 | 0.14 |
132 | 132 | 0.479 |
133 | 133 | 0.886 |
134 | 134 | 0.549 |
135 | 135 | 0.0675 |
136 | 136 | 0.731 |
137 | 137 | 0.282 |
138 | 138 | 0.377 |
139 | 139 | 0.252 |
14 | 14 | 0.315 |
140 | 140 | 0.336 |
141 | 141 | 0.529 |
142 | 142 | 0.388 |
143 | 143 | 0.0172 |
144 | 144 | 0.873 |
145 | 145 | 0.874 |
146 | 146 | 0.484 |
147 | 147 | 0.377 |
148 | 148 | 0.174 |
149 | 149 | 0.0229 |
15 | 15 | 0.424 |
150 | 150 | 0.968 |
151 | 151 | 0.123 |
152 | 152 | 0.00677 |
153 | 153 | 0.822 |
154 | 154 | 0.777 |
155 | 155 | 0.995 |
156 | 156 | 0.708 |
157 | 157 | 0.651 |
158 | 158 | 0.192 |
159 | 159 | 0.223 |
16 | 16 | 0.844 |
160 | 160 | 0.975 |
161 | 161 | 0.115 |
162 | 162 | 0.395 |
163 | 163 | 0.919 |
164 | 164 | 0.438 |
165 | 165 | 0.0429 |
166 | 166 | 0.261 |
167 | 167 | 0.57 |
168 | 168 | 0.101 |
169 | 169 | 0.184 |
17 | 17 | 0.333 |
18 | 18 | 0.166 |
19 | 19 | 0.499 |
2 | 2 | 0.109 |
20 | 20 | 0.278 |
21 | 21 | 0.72 |
22 | 22 | 0.261 |
23 | 23 | 0.00113 |
24 | 24 | 0.294 |
25 | 25 | 0.711 |
26 | 26 | 0.451 |
27 | 27 | 0.102 |
28 | 28 | 0.831 |
29 | 29 | 0.596 |
3 | 3 | 0.437 |
30 | 30 | 0.0996 |
31 | 31 | 0.721 |
32 | 32 | 0.105 |
33 | 33 | 0.795 |
34 | 34 | 0.24 |
35 | 35 | 0.589 |
36 | 36 | 0.975 |
37 | 37 | 0.587 |
38 | 38 | 0.625 |
39 | 39 | 0.291 |
4 | 4 | 0.798 |
40 | 40 | 0.857 |
41 | 41 | 0.0354 |
42 | 42 | 0.137 |
43 | 43 | 0.189 |
44 | 44 | 0.972 |
45 | 45 | 0.103 |
46 | 46 | 0.838 |
47 | 47 | 0.681 |
48 | 48 | 0.938 |
49 | 49 | 0.817 |
5 | 5 | 0.259 |
50 | 50 | 0.53 |
51 | 51 | 0.59 |
52 | 52 | 0.0375 |
53 | 53 | 0.844 |
54 | 54 | 0.483 |
55 | 55 | 0.625 |
56 | 56 | 0.624 |
57 | 57 | 0.297 |
58 | 58 | 0.273 |
59 | 59 | 0.0645 |
6 | 6 | 0.397 |
60 | 60 | 0.011 |
61 | 61 | 0.818 |
62 | 62 | 0.205 |
63 | 63 | 0.269 |
64 | 64 | 0.698 |
65 | 65 | 0.379 |
66 | 66 | 0.0468 |
67 | 67 | 0.988 |
68 | 68 | 0.148 |
69 | 69 | 0.809 |
7 | 7 | 0.802 |
70 | 70 | 0.263 |
71 | 71 | 0.751 |
72 | 72 | 0.576 |
73 | 73 | 0.0862 |
74 | 74 | 0.47 |
75 | 75 | 0.179 |
76 | 76 | 0.696 |
77 | 77 | 0.344 |
78 | 78 | 0.442 |
79 | 79 | 0.069 |
8 | 8 | 0.807 |
80 | 80 | 0.0336 |
81 | 81 | 0.767 |
82 | 82 | 0.058 |
83 | 83 | 0.286 |
84 | 84 | 0.479 |
85 | 85 | 0.0879 |
86 | 86 | 0.996 |
87 | 87 | 0.89 |
88 | 88 | 0.821 |
89 | 89 | 0.445 |
9 | 9 | 0.0434 |
90 | 90 | 0.395 |
91 | 91 | 0.168 |
92 | 92 | 0.213 |
93 | 93 | 0.217 |
94 | 94 | 0.311 |
95 | 95 | 0.184 |
96 | 96 | 0.671 |
97 | 97 | 0.71 |
98 | 98 | 0.83 |
99 | 99 | 0.665 |
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: CNhs11877
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human sample
FF:0102267 rhabdomyosarcoma cell line 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
0050687 (cell type cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
162 (cancer)
4 (disease)
UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)
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