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FF:1389-42C2

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Name:muscle (biceps femoris), neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11129
Sample type:developmental
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuemuscle (biceps femoris)
dev stage30 days neonate
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

Accession numbers
MethodSample accession id
CAGE  SAMD00005267
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11129 CAGE DRX009048 DRR009922
Accession ID Mm9

Library idBAMCTSS
CNhs11129 DRZ001347 DRZ002730
Accession ID Mm10

Library idBAMCTSS
CNhs11129 DRZ012697 DRZ014080
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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

CNhs11129

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 1.074
1001 0.642
1002 --0.0962
1003 0.377
1004 0
1005 0.0416
1006 0.954
1007 --0.0837
1008 0
1009 0.103
101 --0.0491
1010 0
1011 --0.108
1012 0
1013 --0.0449
1014 0
1015 --0.264
1016 0.016
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.968
1023 0
1024 0.373
1025 0
1026 0
1027 0.178
1028 0
1029 --0.115
103 0.625
1030 0.0978
1031 --0.0564
1032 0.277
1033 0
1034 0
1035 0.0978
1036 --0.248
1037 0
1038 0.0487
1039 0.551
104 0
1040 0.0739
1041 0.702



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



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: CNhs11129

Jaspar motif P-value
MA0002.2 0.943
MA0003.1 0.093
MA0004.1 0.221
MA0006.1 0.133
MA0007.1 0.309
MA0009.1 0.99
MA0014.1 0.993
MA0017.1 0.745
MA0018.2 0.0147
MA0019.1 0.115
MA0024.1 2.30827e-5
MA0025.1 0.151
MA0027.1 0.385
MA0028.1 0.0087
MA0029.1 0.582
MA0030.1 0.884
MA0031.1 0.313
MA0035.2 0.328
MA0038.1 0.932
MA0039.2 0.532
MA0040.1 0.858
MA0041.1 0.156
MA0042.1 0.666
MA0043.1 0.0734
MA0046.1 1.1464e-14
MA0047.2 0.483
MA0048.1 0.0341
MA0050.1 0.168
MA0051.1 0.609
MA0052.1 3.12094e-65
MA0055.1 0.177
MA0057.1 0.683
MA0058.1 0.205
MA0059.1 0.0838
MA0060.1 3.09661e-6
MA0061.1 0.947
MA0062.2 6.90819e-7
MA0065.2 0.00554
MA0066.1 0.317
MA0067.1 0.502
MA0068.1 0.129
MA0069.1 0.17
MA0070.1 0.744
MA0071.1 0.00813
MA0072.1 0.308
MA0073.1 0.159
MA0074.1 0.601
MA0076.1 9.27111e-4
MA0077.1 0.239
MA0078.1 0.0947
MA0079.2 0.345
MA0080.2 6.58674e-4
MA0081.1 0.833
MA0083.1 5.62276e-7
MA0084.1 0.945
MA0087.1 0.861
MA0088.1 0.691
MA0090.1 0.0831
MA0091.1 0.029
MA0092.1 0.148
MA0093.1 0.198
MA0099.2 0.791
MA0100.1 0.0295
MA0101.1 0.256
MA0102.2 0.329
MA0103.1 0.0123
MA0104.2 0.0486
MA0105.1 0.827
MA0106.1 0.937
MA0107.1 0.35
MA0108.2 1.3671e-5
MA0111.1 0.782
MA0112.2 3.58765e-7
MA0113.1 0.078
MA0114.1 0.781
MA0115.1 0.844
MA0116.1 0.484
MA0117.1 0.575
MA0119.1 0.474
MA0122.1 0.239
MA0124.1 0.222
MA0125.1 0.606
MA0131.1 0.51
MA0135.1 0.714
MA0136.1 5.71564e-6
MA0137.2 0.0149
MA0138.2 0.0043
MA0139.1 0.524
MA0140.1 0.817
MA0141.1 1.21142e-7
MA0142.1 0.594
MA0143.1 0.202
MA0144.1 0.41
MA0145.1 0.0229
MA0146.1 0.0697
MA0147.1 0.117
MA0148.1 0.586
MA0149.1 0.328
MA0150.1 0.0504
MA0152.1 0.896
MA0153.1 4.14602e-10
MA0154.1 0.0414
MA0155.1 0.153
MA0156.1 1.60854e-6
MA0157.1 0.3
MA0159.1 0.00433
MA0160.1 2.61104e-4
MA0162.1 0.222
MA0163.1 0.0612
MA0164.1 0.35
MA0258.1 1.30285e-5
MA0259.1 0.198



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: CNhs11129

Novel motif P-value
1 0.201
10 0.678
100 0.418
101 0.394
102 0.574
103 0.784
104 0.999
105 0.0893
106 0.18
107 0.253
108 0.763
109 0.0667
11 0.162
110 0.391
111 0.438
112 0.733
113 0.649
114 0.168
115 0.431
116 0.38
117 0.881
118 0.486
119 0.0465
12 0.117
120 0.892
121 0.563
122 0.97
123 0.665
124 0.227
125 0.474
126 0.893
127 0.171
128 0.469
129 0.338
13 0.00372
130 0.721
131 0.708
132 0.896
133 0.726
134 0.473
135 0.478
136 0.292
137 0.899
138 0.23
139 0.0864
14 0.124
140 0.06
141 0.09
142 0.978
143 0.733
144 0.106
145 0.923
146 0.761
147 0.797
148 0.851
149 0.0608
15 0.847
150 0.454
151 0.257
152 0.0387
153 0.363
154 0.934
155 0.681
156 0.115
157 0.283
158 0.981
159 0.338
160 0.239
161 0.126
162 0.511
163 0.402
164 0.727
165 0.00975
166 0.801
167 0.191
168 0.0819
169 5.68599e-4
17 0.131
18 0.975
19 0.0232
2 0.359
20 0.914
21 0.823
22 0.0514
23 0.399
24 0.926
25 0.727
26 0.368
27 0.863
28 0.79
29 0.988
3 0.563
30 0.803
31 0.213
32 0.0295
33 0.796
34 0.171
35 0.767
36 0.197
37 0.00948
38 0.701
39 0.338
4 0.705
40 0.573
41 0.397
42 0.571
43 0.271
44 0.562
45 0.31
46 0.408
47 0.99
48 0.671
49 0.669
5 0.145
50 0.317
51 0.879
52 0.34
53 0.692
54 0.383
55 0.308
56 0.456
57 0.365
58 0.683
59 0.00747
6 0.52
60 0.0993
61 0.777
62 0.305
63 0.0709
64 0.724
65 0.453
66 0.738
67 0.273
68 0.587
69 0.0159
7 0.136
70 0.116
71 0.104
72 0.652
73 0.0239
74 0.151
75 0.586
76 0.536
77 0.436
78 0.0172
79 0.0755
8 0.363
80 0.469
81 0.152
82 0.106
83 0.413
84 0.581
85 0.00135
86 0.194
87 0.319
88 0.812
89 0.0782
9 0.462
90 0.326
91 0.192
92 0.484
93 0.294
94 0.237
95 0.149
96 0.399
97 0.911
98 0.662
99 0.68



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: CNhs11129


FANTOM5 (FF) ontology


Direct parent terms


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
0000468 (multi-cellular organism)
0001374 (biceps femoris)
0000479 (tissue)
0000062 (organ)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0002472 (stylopod)
0008784 (lower limb segment)
0001062 (anatomical entity)
0000480 (anatomical group)
0006058 (multi-limb segment region)
0004252 (hindlimb stylopod muscle)
0003663 (hindlimb muscle)
0005090 (muscle structure)
0001630 (muscle organ)
0004708 (paired limb/fin)
0002101 (limb)
0004709 (pelvic appendage)
0002529 (limb segment)
0010538 (paired limb/fin segment)
0003661 (limb muscle)
0010890 (pelvic complex muscle)
0010317 (germ layer / neural crest derived structure)
0001383 (muscle of leg)
0010758 (subdivision of organism along appendicular axis)
0010707 (appendage girdle complex)
0002204 (musculoskeletal system)
0000978 (leg)
0002103 (hindlimb)
0000376 (hindlimb stylopod)
0000383 (musculature of body)
0000154 (posterior region of body)
0010709 (pelvic complex)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011490 (mouse muscle - biceps femoris- neonate N30 sample)

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

link to source data
data

UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)