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|top_motifs=HOX{A5,B5}:3.25770262386;EVI1:2.74239457396;MEF2{A,B,C,D}:2.74129535873;GATA4:2.60198871133;NR5A1,2:2.51422250775;SRF:2.18360698325;HIF1A:1.77002527716;IKZF2:1.74831723024;NKX2-1,4:1.74471732868;FOXL1:1.6564236242;RXR{A,B,G}:1.61980426147;TEAD1:1.5338219603;NFE2L1:1.35849228675;PRDM1:1.27789259339;HMGA1,2:1.2443247768;NR3C1:1.24352602947;POU3F1..4:1.17004300561;T:1.14701061968;ALX1:1.14321213268;UFEwm:1.01968896849;NANOG{mouse}:1.00710712051;GATA6:0.985121823835;SOX{8,9,10}:0.959683101906;NKX2-2,8:0.947686106319;SOX5:0.923230331755;TGIF1:0.92013325949;KLF4:0.884992873391;PAX4:0.798753548307;MYBL2:0.746095200654;NFATC1..3:0.721129414039;IKZF1:0.70687596543;GFI1:0.701965779936;MZF1:0.698851304437;ESRRA:0.695397671753;ZNF143:0.684213075245;PITX1..3:0.680885026765;FOXP1:0.665686272581;E2F1..5:0.598914269668;TLX1..3_NFIC{dimer}:0.535900517474;HBP1_HMGB_SSRP1_UBTF:0.526613542876;NR6A1:0.519621080972;GCM1,2:0.516718606786;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.501159682175;CDX1,2,4:0.497038422975;EP300:0.469774806499;CUX2:0.4541504311;RREB1:0.423685977142;TOPORS:0.405270534734;ZNF384:0.385271362791;EN1,2:0.376719556014;PATZ1:0.371683889977;AR:0.365975267638;GFI1B:0.364372309558;TEF:0.348375093667;CDC5L:0.329196890593;NRF1:0.28571670166;SPIB:0.277464463417;ZBTB16:0.271093808011;EBF1:0.262754204762;MAFB:0.262369843015;SOX17:0.24624569687;SMAD1..7,9:0.221612151039;BREu{core}:0.219308069333;MAZ:0.212499615992;PAX2:0.187714522271;FOSL2:0.184285992135;NFE2L2:0.174126643872;NKX3-1:0.174016710639;TFAP4:0.138816392127;NFY{A,B,C}:0.122764445633;ARID5B:0.0930207168507;TFCP2:0.0926949266515;NKX6-1,2:0.0863866077239;ZNF238:0.0777224468528;FOX{I1,J2}:0.0711666870938;SOX2:0.0631122731064;PAX5:0.0622886366514;SP1:0.0453776765463;ELF1,2,4:0.0379946619679;PDX1:0.0156717726775;ATF2:-0.028584535438;XCPE1{core}:-0.0417297308904;FOXD3:-0.0542830911142;FOXO1,3,4:-0.0554664021717;ZFP161:-0.0580016854801;TFAP2B:-0.0740500351104;SPI1:-0.0822038630488;GTF2A1,2:-0.0941305715896;CRX:-0.113936392572;VSX1,2:-0.11690122674;NANOG:-0.117626726966;CREB1:-0.126404275375;ZIC1..3:-0.138242217621;NKX3-2:-0.140224551246;NKX2-3_NKX2-5:-0.141393774679;MYB:-0.14476642859;DBP:-0.152103884313;GLI1..3:-0.157108780855;MTE{core}:-0.159079201723;TBP:-0.165022858249;TFDP1:-0.167001322531;RFX2..5_RFXANK_RFXAP:-0.169125170453;YY1:-0.170205426001;ELK1,4_GABP{A,B1}:-0.192328637553;POU1F1:-0.22394412904;NHLH1,2:-0.224731491361;ATF4:-0.224736476384;GTF2I:-0.226068411504;ETS1,2:-0.226580277952;HOX{A4,D4}:-0.231817415257;EGR1..3:-0.247695027553;TFAP2{A,C}:-0.249693208044;HIC1:-0.252310789596;ZNF423:-0.268907256458;AIRE:-0.2783638153;PAX8:-0.28868248836;HAND1,2:-0.316531013504;SREBF1,2:-0.32556546448;BPTF:-0.331558801685;FOXA2:-0.364344313092;RORA:-0.370169266176;ESR1:-0.374023960955;RBPJ:-0.389511018277;PAX1,9:-0.397127499912;JUN:-0.416676566633;MTF1:-0.419327486358;FOXP3:-0.423398369978;IRF1,2:-0.429371381386;TLX2:-0.479482522646;ALX4:-0.482351889933;RFX1:-0.48662694719;MED-1{core}:-0.489684400297;IRF7:-0.500072534805;ZNF148:-0.511747673549;HSF1,2:-0.523610475358;HOXA9_MEIS1:-0.532911763065;FOX{D1,D2}:-0.551312083198;ZBTB6:-0.562871309017;TP53:-0.586212890827;OCT4_SOX2{dimer}:-0.601508408552;RUNX1..3:-0.626628367064;GZF1:-0.628675214517;DMAP1_NCOR{1,2}_SMARC:-0.628928098803;NFIL3:-0.631488735878;AHR_ARNT_ARNT2:-0.634442722965;HNF1A:-0.63550248229;ONECUT1,2:-0.637999812707;HES1:-0.647515384684;HNF4A_NR2F1,2:-0.654224467997;NFKB1_REL_RELA:-0.666202245874;RXRA_VDR{dimer}:-0.668632965982;POU5F1:-0.673670909035;STAT1,3:-0.684384535031;REST:-0.685696534377;TBX4,5:-0.711930683021;PAX6:-0.718269381616;LHX3,4:-0.75596141917;NFE2:-0.787099854176;NFIX:-0.794321917972;POU6F1:-0.798547683077;MYFfamily:-0.83281814611;BACH2:-0.83289005557;bHLH_family:-0.838926315469;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.846607999292;NR1H4:-0.865518278578;FOXN1:-0.910840587353;ATF5_CREB3:-0.928525638472;SNAI1..3:-0.935501268844;HMX1:-0.936869721909;FOX{F1,F2,J1}:-0.943706303609;FOS_FOS{B,L1}_JUN{B,D}:-0.960182823293;HLF:-0.963158885676;ZEB1:-0.999227803939;ADNP_IRX_SIX_ZHX:-1.03679678575;POU2F1..3:-1.06565390738;LEF1_TCF7_TCF7L1,2:-1.07299569231;PBX1:-1.08581542837;PRRX1,2:-1.11778750524;LMO2:-1.13473671468;SPZ1:-1.13861660656;MYOD1:-1.14473612451;FOXQ1:-1.15673053333;ATF6:-1.20734238168;CEBPA,B_DDIT3:-1.22845966073;TAL1_TCF{3,4,12}:-1.34271392337;STAT5{A,B}:-1.44842806432;STAT2,4,6:-1.50165645712;PPARG:-1.848113563;FOXM1:-1.99471937794
 
}}
 
}}

Revision as of 06:19, 15 February 2012


Name:heart, embryo E15, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueheart
dev stage15 days embryo
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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

CNhs11017

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0.201
100 0
1000 0.253
1001 0.343
1002 0.406
1003 --0.0271
1004 0
1005 0
1006 0.235
1007 0.0231
1008 0
1009 0.211
101 0.00274
1010 0
1011 -2.590399e-4
1012 0
1013 --0.297
1014 0.523
1015 0.0902
1016 0.165
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.552
1023 0
1024 0.165
1025 0
1026 0
1027 0
1028 0
1029 0.0762
103 0.0539
1030 0
1031 0.358
1032 0.034
1033 --0.0752
1034 0
1035 0.575
1036 0.0449
1037 0
1038 0.102
1039 0.0664
104 0
1040 0.115
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: CNhs11017

Jaspar motif P-value
MA0002.2 0.0238
MA0003.1 0.55
MA0004.1 0.276
MA0006.1 0.886
MA0007.1 0.0901
MA0009.1 0.669
MA0014.1 0.527
MA0017.1 0.00966
MA0018.2 0.103
MA0019.1 0.558
MA0024.1 0.00262
MA0025.1 0.208
MA0027.1 0.098
MA0028.1 0.668
MA0029.1 0.505
MA0030.1 0.0656
MA0031.1 0.0971
MA0035.2 0.21
MA0038.1 0.883
MA0039.2 0.034
MA0040.1 0.044
MA0041.1 0.249
MA0042.1 0.396
MA0043.1 0.436
MA0046.1 8.0487e-16
MA0047.2 0.0222
MA0048.1 0.0214
MA0050.1 1.59763e-4
MA0051.1 0.0185
MA0052.1 3.60077e-28
MA0055.1 2.53487e-4
MA0057.1 0.818
MA0058.1 0.428
MA0059.1 0.901
MA0060.1 0.91
MA0061.1 0.28
MA0062.2 0.00705
MA0065.2 0.201
MA0066.1 0.72
MA0067.1 0.395
MA0068.1 0.195
MA0069.1 0.285
MA0070.1 0.534
MA0071.1 0.926
MA0072.1 0.143
MA0073.1 0.871
MA0074.1 0.696
MA0076.1 0.16
MA0077.1 0.839
MA0078.1 0.296
MA0079.2 0.72
MA0080.2 0.0313
MA0081.1 0.941
MA0083.1 1.32254e-14
MA0084.1 0.801
MA0087.1 0.751
MA0088.1 0.556
MA0090.1 0.00245
MA0091.1 0.774
MA0092.1 0.832
MA0093.1 0.31
MA0099.2 6.11104e-8
MA0100.1 0.792
MA0101.1 0.503
MA0102.2 0.00433
MA0103.1 1.3511e-6
MA0104.2 0.702
MA0105.1 0.578
MA0106.1 0.848
MA0107.1 0.498
MA0108.2 0.695
MA0111.1 0.548
MA0112.2 0.152
MA0113.1 0.568
MA0114.1 1.50481e-4
MA0115.1 0.833
MA0116.1 0.317
MA0117.1 0.236
MA0119.1 0.0372
MA0122.1 0.841
MA0124.1 0.408
MA0125.1 0.735
MA0131.1 0.963
MA0135.1 0.266
MA0136.1 0.0225
MA0137.2 0.0217
MA0138.2 0.24
MA0139.1 0.541
MA0140.1 0.148
MA0141.1 6.26454e-5
MA0142.1 0.237
MA0143.1 0.945
MA0144.1 0.186
MA0145.1 0.282
MA0146.1 0.945
MA0147.1 0.665
MA0148.1 0.0571
MA0149.1 0.116
MA0150.1 0.00334
MA0152.1 0.973
MA0153.1 4.81962e-11
MA0154.1 0.59
MA0155.1 0.24
MA0156.1 6.13926e-4
MA0157.1 0.237
MA0159.1 0.141
MA0160.1 0.0727
MA0162.1 0.0922
MA0163.1 0.198
MA0164.1 0.363
MA0258.1 0.717
MA0259.1 0.389



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: CNhs11017

Novel motif P-value
1 0.982
10 0.869
100 0.725
101 0.883
102 0.667
103 0.435
104 0.927
105 0.672
106 0.373
107 0.952
108 0.978
109 0.772
11 0.463
110 0.175
111 0.52
112 0.267
113 0.583
114 0.652
115 0.834
116 0.344
117 0.423
118 0.249
119 0.607
12 0.6
120 0.144
121 0.923
122 0.28
123 0.101
124 0.756
125 0.836
126 0.947
127 0.226
128 0.0439
129 0.864
13 0.00168
130 0.375
131 0.478
132 0.687
133 0.638
134 0.737
135 0.914
136 0.0743
137 0.502
138 0.164
139 0.605
14 0.923
140 0.669
141 0.365
142 0.8
143 0.512
144 0.119
145 0.0756
146 0.332
147 0.756
148 0.871
149 0.739
15 0.32
150 0.329
151 0.148
152 0.754
153 0.566
154 0.704
155 0.297
156 0.0189
157 0.596
158 0.36
159 0.0869
160 0.31
161 0.748
162 0.915
163 0.99
164 0.734
165 0.108
166 0.586
167 0.794
168 0.574
169 0.00506
17 0.288
18 0.104
19 0.246
2 0.343
20 0.247
21 0.739
22 0.447
23 0.284
24 0.614
25 0.473
26 0.0049
27 0.215
28 0.221
29 0.969
3 0.819
30 0.0391
31 0.461
32 0.505
33 0.111
34 0.528
35 0.25
36 0.138
37 0.272
38 0.585
39 0.455
4 0.513
40 0.00333
41 0.863
42 0.606
43 0.863
44 0.75
45 0.0453
46 0.951
47 0.843
48 0.954
49 0.569
5 0.973
50 0.525
51 0.953
52 0.695
53 0.741
54 0.654
55 0.183
56 0.766
57 0.323
58 0.886
59 0.324
6 0.0687
60 0.762
61 0.4
62 0.564
63 0.759
64 0.577
65 0.456
66 0.578
67 0.786
68 0.175
69 0.277
7 0.357
70 0.00975
71 0.0157
72 0.0814
73 0.547
74 0.891
75 0.33
76 0.544
77 0.617
78 0.393
79 0.373
8 0.712
80 0.0118
81 0.461
82 0.903
83 0.785
84 0.81
85 0.383
86 0.673
87 4.03396e-5
88 0.349
89 0.114
9 0.557
90 0.823
91 0.117
92 0.25
93 0.229
94 0.261
95 0.607
96 0.359
97 0.157
98 0.357
99 0.455



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: CNhs11017


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

UBERON: Anatomy
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000948 (heart)
0001009 (circulatory system)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003084 (heart primordium)
0003914 (epithelial tube)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
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)

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