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|top_motifs=UFEwm:1.85086367274;IKZF1:1.84473079887;NFE2L2:1.67005209663;TEAD1:1.54863911308;GLI1..3:1.50686672649;NR3C1:1.50569621648;NFE2:1.50255800562;STAT2,4,6:1.48436294905;ZNF238:1.43431370629;HIF1A:1.36581436959;NFE2L1:1.25274972913;TP53:1.23743594594;BACH2:1.23500614208;NKX3-1:1.20332125867;FOXP3:1.15608521298;TLX1..3_NFIC{dimer}:1.13424442965;AR:1.12010748325;MTE{core}:1.10781650355;GCM1,2:1.10704302162;CEBPA,B_DDIT3:1.07584322796;HAND1,2:1.07297119021;FOS_FOS{B,L1}_JUN{B,D}:1.05769768077;ESR1:1.04548958853;NFATC1..3:1.00284764629;DBP:0.991745975577;EVI1:0.954148498812;HES1:0.944975808552;HOXA9_MEIS1:0.920920051912;CDC5L:0.918927930221;T:0.91534130211;DMAP1_NCOR{1,2}_SMARC:0.879893011291;TFAP4:0.87136801364;SRF:0.867123463644;ATF4:0.842415538825;TAL1_TCF{3,4,12}:0.746569080166;TFCP2:0.745697213721;ALX4:0.71429270882;FOSL2:0.702375774181;MYBL2:0.687144941697;ALX1:0.686443577175;ATF6:0.658714971893;HMGA1,2:0.599794750429;IRF7:0.582929975121;ELF1,2,4:0.561585721715;EP300:0.547255955855;TFAP2{A,C}:0.531049057568;HBP1_HMGB_SSRP1_UBTF:0.522637458479;NR1H4:0.490033416763;HOX{A5,B5}:0.48888603218;HLF:0.46367892494;IKZF2:0.455818791448;NFKB1_REL_RELA:0.44610359709;ZNF148:0.433056460453;ELK1,4_GABP{A,B1}:0.431080806467;PAX8:0.401768552202;GATA4:0.387046379126;RXRA_VDR{dimer}:0.375756038206;XCPE1{core}:0.358157469361;MAZ:0.337914366107;GTF2A1,2:0.333611105514;ZNF423:0.329547526232;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.315787349344;IRF1,2:0.29077693809;NKX2-2,8:0.284199823097;MAFB:0.268710960125;GZF1:0.267305426012;PAX2:0.266302445549;GTF2I:0.262726561157;SREBF1,2:0.260167730366;NFIL3:0.256399645315;FOXL1:0.255625142135;SPI1:0.210852513413;PDX1:0.196377823262;RXR{A,B,G}:0.191746703107;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.181067161392;GFI1B:0.173129928272;ETS1,2:0.158547539364;EBF1:0.15791174039;HMX1:0.149046784442;POU2F1..3:0.146487736579;SOX17:0.144609508257;EN1,2:0.140219295567;POU1F1:0.140145244394;TOPORS:0.133602162014;LHX3,4:0.133081959623;EGR1..3:0.123122070902;KLF4:0.118966261116;PAX5:0.1165943454;HSF1,2:0.116352445341;SP1:0.109820784272;PAX4:0.0921406500113;SPIB:0.0529820307113;SPZ1:0.0485493050734;HIC1:0.0182977574145;CREB1:0.0040362002277;RUNX1..3:-0.0144656563937;MTF1:-0.027813214784;RREB1:-0.0279410242811;ONECUT1,2:-0.0344339915805;NHLH1,2:-0.0357504212476;STAT1,3:-0.0558931878139;CDX1,2,4:-0.0569438520212;ZIC1..3:-0.0685557717332;SMAD1..7,9:-0.076443072244;PATZ1:-0.106202184603;NKX2-3_NKX2-5:-0.109528451982;ZBTB6:-0.116936138527;ATF2:-0.125115307826;MYB:-0.131619860264;TFAP2B:-0.162785291427;BPTF:-0.242777542588;NKX2-1,4:-0.244439689267;PRDM1:-0.264053255943;FOX{D1,D2}:-0.300910935278;TBP:-0.305085643106;FOXO1,3,4:-0.308135290842;ZFP161:-0.321504949269;PAX1,9:-0.331052028016;TEF:-0.341414485893;SOX5:-0.351581517864;POU3F1..4:-0.365957271578;ATF5_CREB3:-0.370882049685;MEF2{A,B,C,D}:-0.384514955926;AHR_ARNT_ARNT2:-0.395757607765;MED-1{core}:-0.400499614672;E2F1..5:-0.402578760102;RFX1:-0.410889134631;CRX:-0.423182304241;FOXD3:-0.424500465476;JUN:-0.438868302947;HNF4A_NR2F1,2:-0.451102889449;REST:-0.453849942344;ZNF384:-0.474780577145;ZBTB16:-0.476939923862;FOX{I1,J2}:-0.500416073805;PAX6:-0.51632939898;MZF1:-0.522116788521;HOX{A4,D4}:-0.522975051049;SOX2:-0.527538950016;RORA:-0.532950350955;HNF1A:-0.554436398783;ARID5B:-0.565977352573;TLX2:-0.570633991236;RFX2..5_RFXANK_RFXAP:-0.591183646994;MYFfamily:-0.594165344873;POU5F1:-0.597958524522;ESRRA:-0.607359503724;AIRE:-0.620226555064;TFDP1:-0.623031504263;FOXP1:-0.685271112857;YY1:-0.690801603766;GATA6:-0.724203355648;ADNP_IRX_SIX_ZHX:-0.725179640461;LEF1_TCF7_TCF7L1,2:-0.735430600442;bHLH_family:-0.791942315495;NKX3-2:-0.793515453059;TBX4,5:-0.799351917659;NRF1:-0.800802879741;NR6A1:-0.807321757426;PPARG:-0.810168872105;FOXA2:-0.813151209708;PITX1..3:-0.817299913158;NANOG{mouse}:-0.818734464802;NKX6-1,2:-0.822818304223;FOXN1:-0.823828894855;FOXQ1:-0.849677818244;RBPJ:-0.866881180298;TGIF1:-0.891098500071;PRRX1,2:-0.910003137474;FOXM1:-0.970819150243;ZNF143:-0.97392963786;FOX{F1,F2,J1}:-0.975358689859;STAT5{A,B}:-0.985226570989;NR5A1,2:-0.986801353289;VSX1,2:-1.03422295382;GFI1:-1.08989126033;NANOG:-1.12083324642;BREu{core}:-1.15180328196;NFIX:-1.15490932776;OCT4_SOX2{dimer}:-1.23383423433;NFY{A,B,C}:-1.28131486871;SOX{8,9,10}:-1.33690142309;SNAI1..3:-1.60308802204;CUX2:-1.68902376131;PBX1:-1.7608105934;ZEB1:-1.79878040143;MYOD1:-1.90531514213;POU6F1:-1.99967629854;LMO2:-2.56376230373
 
}}
 
}}

Revision as of 06:17, 15 February 2012


Name:Mouse Cardiac Myocytes, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueheart
dev stageNA
sexNA
ageNA
cell typecardiac muscle cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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.
Analyst:NA

link to dataset.
data

CNhs12355

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0639
1001 --0.00986
1002 0.425
1003 0.14
1004 0
1005 0
1006 --0.302
1007 --0.201
1008 0
1009 0.56
101 --0.0743
1010 0
1011 --0.198
1012 0
1013 0.0555
1014 0.00488
1015 --0.0304
1016 0.106
1017 0
1018 0
1019 0
102 0
1020 0.18
1021 0.0994
1022 --0.0704
1023 0
1024 --0.14
1025 0
1026 0
1027 0
1028 0.0994
1029 --0.12
103 0.549
1030 0
1031 0.732
1032 0.0785
1033 --0.0752
1034 0
1035 0
1036 --0.0803
1037 0
1038 -5.64625e-4
1039 --0.154
104 0
1040 0.526
1041 0



Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data
no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs12355

Jaspar motif P-value
MA0002.2 0.314
MA0003.1 0.305
MA0004.1 0.863
MA0006.1 0.203
MA0007.1 0.00826
MA0009.1 0.735
MA0014.1 0.392
MA0017.1 0.00911
MA0018.2 0.0607
MA0019.1 0.458
MA0024.1 0.00165
MA0025.1 0.727
MA0027.1 0.187
MA0028.1 0.11
MA0029.1 0.806
MA0030.1 0.209
MA0031.1 0.43
MA0035.2 0.0121
MA0038.1 0.1
MA0039.2 0.115
MA0040.1 0.0315
MA0041.1 0.473
MA0042.1 0.686
MA0043.1 0.54
MA0046.1 3.88064e-9
MA0047.2 0.0084
MA0048.1 0.0733
MA0050.1 0.0038
MA0051.1 0.125
MA0052.1 0.27
MA0055.1 0.0107
MA0057.1 0.0583
MA0058.1 0.648
MA0059.1 0.64
MA0060.1 1.52606e-10
MA0061.1 0.131
MA0062.2 0.0877
MA0065.2 0.807
MA0066.1 0.492
MA0067.1 0.841
MA0068.1 0.0423
MA0069.1 0.238
MA0070.1 0.626
MA0071.1 0.569
MA0072.1 0.923
MA0073.1 0.332
MA0074.1 0.503
MA0076.1 0.571
MA0077.1 0.846
MA0078.1 0.496
MA0079.2 0.00735
MA0080.2 0.289
MA0081.1 0.708
MA0083.1 1.65715e-4
MA0084.1 0.545
MA0087.1 0.712
MA0088.1 0.516
MA0090.1 2.72667e-4
MA0091.1 0.0523
MA0092.1 0.164
MA0093.1 0.812
MA0099.2 5.91583e-9
MA0100.1 0.985
MA0101.1 0.0114
MA0102.2 0.646
MA0103.1 6.49974e-7
MA0104.2 0.239
MA0105.1 0.405
MA0106.1 4.17265e-4
MA0107.1 0.0249
MA0108.2 0.0793
MA0111.1 0.927
MA0112.2 0.0181
MA0113.1 0.0218
MA0114.1 0.02
MA0115.1 0.0909
MA0116.1 0.776
MA0117.1 0.238
MA0119.1 0.171
MA0122.1 0.745
MA0124.1 0.253
MA0125.1 0.0292
MA0131.1 0.559
MA0135.1 0.343
MA0136.1 0.35
MA0137.2 0.299
MA0138.2 0.00114
MA0139.1 0.432
MA0140.1 0.0253
MA0141.1 0.287
MA0142.1 0.012
MA0143.1 0.709
MA0144.1 0.0091
MA0145.1 0.0534
MA0146.1 0.0195
MA0147.1 0.263
MA0148.1 0.0864
MA0149.1 0.966
MA0150.1 0.00453
MA0152.1 0.827
MA0153.1 3.88925e-8
MA0154.1 0.0423
MA0155.1 0.915
MA0156.1 0.0268
MA0157.1 0.386
MA0159.1 0.171
MA0160.1 0.269
MA0162.1 0.195
MA0163.1 0.174
MA0164.1 0.706
MA0258.1 0.565
MA0259.1 0.983



FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs12355

Novel motif P-value
1 0.879
10 0.222
100 0.478
101 0.395
102 0.128
103 0.817
104 0.233
105 0.402
106 0.0116
107 0.369
108 0.564
109 0.0228
11 0.474
110 0.199
111 0.856
112 0.94
113 0.471
114 0.282
115 0.957
116 0.0829
117 0.0643
118 0.886
119 0.679
12 0.912
120 0.402
121 0.353
122 0.0654
123 0.795
124 0.494
125 0.118
126 0.119
127 0.0399
128 0.0261
129 0.241
13 0.0737
130 0.991
131 0.0884
132 0.188
133 0.201
134 0.82
135 0.756
136 0.033
137 0.718
138 0.904
139 0.817
14 0.334
140 0.507
141 0.318
142 0.826
143 0.0755
144 0.217
145 0.237
146 0.717
147 0.315
148 0.983
149 0.00557
15 0.128
150 0.041
151 0.612
152 0.00866
153 0.744
154 0.768
155 0.186
156 0.997
157 0.451
158 0.698
159 0.0776
160 0.924
161 0.471
162 0.392
163 0.436
164 0.296
165 0.37
166 0.761
167 0.539
168 0.709
169 0.0198
17 0.32
18 0.36
19 0.0392
2 0.383
20 0.221
21 0.14
22 0.139
23 0.324
24 0.0677
25 0.154
26 0.0479
27 0.287
28 0.61
29 0.0278
3 0.377
30 0.36
31 0.807
32 0.154
33 0.95
34 0.957
35 0.255
36 0.556
37 0.0312
38 0.423
39 0.164
4 0.323
40 0.684
41 0.992
42 0.543
43 0.0674
44 0.337
45 0.931
46 0.657
47 0.722
48 0.942
49 0.92
5 0.933
50 0.11
51 0.696
52 0.528
53 0.735
54 0.546
55 0.987
56 0.819
57 0.796
58 0.534
59 0.0171
6 0.429
60 0.465
61 0.362
62 0.954
63 0.352
64 0.37
65 0.224
66 0.796
67 0.81
68 0.145
69 0.984
7 0.957
70 0.0158
71 0.2
72 0.771
73 0.0016
74 0.464
75 0.161
76 0.667
77 0.0415
78 0.023
79 0.223
8 0.623
80 0.0224
81 0.819
82 0.987
83 0.629
84 0.854
85 0.145
86 0.572
87 0.00877
88 0.297
89 0.78
9 0.774
90 0.881
91 0.523
92 0.0978
93 0.575
94 0.796
95 0.00142
96 0.203
97 0.264
98 0.406
99 0.898



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs12355


FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000056 (myoblast)
0000183 (contractile cell)
0000187 (muscle cell)
0000211 (electrically active cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000355 (multi-potent skeletal muscle stem cell)
0000393 (electrically responsive cell)
0000513 (cardiac muscle myoblast)
0000548 (animal cell)
0000680 (muscle precursor cell)
0000723 (somatic stem cell)
0000737 (striated muscle cell)
0000746 (cardiac muscle cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002494 (cardiocyte)

UBERON: Anatomy
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000948 (heart)
0001009 (circulatory system)
0001015 (musculature)
0001048 (primordium)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003081 (lateral plate mesoderm)
0003082 (myotome)
0003084 (heart primordium)
0003104 (mesenchyme)
0003914 (epithelial tube)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004290 (dermomyotome)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0007005 (cardiac mesoderm)
0007100 (primary circulatory organ)
0009142 (entire embryonic mesenchyme)

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

NA