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FF:56-12G2

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Name:bone (os femoris), adult
Species:Mouse (Mus musculus)
Library ID:CNhs10483
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
tissuebone (os femoris)
dev stageadult
sexmale
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  SAMD00006018
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10483 CAGE DRX008936 DRR009810
Accession ID Mm9

Library idBAMCTSS
CNhs10483 DRZ001235 DRZ002618
Accession ID Mm10

Library idBAMCTSS
CNhs10483 DRZ012585 DRZ013968
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked 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

CNhs10483

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.693
1001 0.0264
1002 -0.116
1003 -0.0139
1004 0
1005 0.5
1006 0.351
1007 -0.0321
1008 0
1009 -0.19
101 -0.032
1010 0
1011 0
1012 0
1013 0.104
1014 -0.0874
1015 -0.0806
1016 -0.389
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.151
1023 0
1024 0.136
1025 0
1026 0
1027 0
1028 0
1029 -0.148
103 0.275
1030 0
1031 -0.458
1032 -0.294
1033 0
1034 0
1035 0
1036 0.0919
1037 0
1038 -0.109
1039 -0.0731
104 0
1040 -0.216
1041 0.275



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs10483
Jaspar motif P-value
MA0002.2 4.08556e-8
MA0003.1 0.0296
MA0004.1 0.551
MA0006.1 0.164
MA0007.1 0.531
MA0009.1 0.697
MA0014.1 0.752
MA0017.1 0.478
MA0018.2 0.00909
MA0019.1 0.273
MA0024.1 0.614
MA0025.1 0.809
MA0027.1 0.582
MA0028.1 0.816
MA0029.1 0.724
MA0030.1 0.922
MA0031.1 0.898
MA0035.2 1.94937e-5
MA0038.1 0.0242
MA0039.2 0.184
MA0040.1 0.117
MA0041.1 0.276
MA0042.1 0.405
MA0043.1 0.0532
MA0046.1 4.74323e-13
MA0047.2 0.435
MA0048.1 0.375
MA0050.1 7.33306e-6
MA0051.1 1.66842e-5
MA0052.1 2.25739e-10
MA0055.1 0.566
MA0057.1 0.639
MA0058.1 0.351
MA0059.1 0.41
MA0060.1 0.121
MA0061.1 0.0184
MA0062.2 0.186
MA0065.2 0.0341
MA0066.1 0.222
MA0067.1 0.751
MA0068.1 0.0746
MA0069.1 0.383
MA0070.1 0.395
MA0071.1 0.451
MA0072.1 0.416
MA0073.1 0.0988
MA0074.1 0.562
MA0076.1 0.45
MA0077.1 0.0928
MA0078.1 0.825
MA0079.2 0.331
MA0080.2 5.93183e-14
MA0081.1 0.0101
MA0083.1 0.122
MA0084.1 0.157
MA0087.1 0.279
MA0088.1 0.811
MA0090.1 0.495
MA0091.1 0.0523
MA0092.1 0.743
MA0093.1 0.461
MA0099.2 0.0877
MA0100.1 0.304
MA0101.1 0.253
MA0102.2 0.0275
MA0103.1 0.896
MA0104.2 0.334
MA0105.1 5.57347e-4
MA0106.1 0.864
MA0107.1 0.0904
MA0108.2 0.0282
MA0111.1 0.558
MA0112.2 6.03827e-6
MA0113.1 0.589
MA0114.1 0.95
MA0115.1 0.697
MA0116.1 1.64626e-4
MA0117.1 0.602
MA0119.1 0.222
MA0122.1 0.412
MA0124.1 0.866
MA0125.1 0.0293
MA0131.1 0.395
MA0135.1 0.718
MA0136.1 3.64724e-14
MA0137.2 0.588
MA0138.2 0.572
MA0139.1 0.617
MA0140.1 5.67878e-17
MA0141.1 0.316
MA0142.1 0.00543
MA0143.1 0.496
MA0144.1 0.728
MA0145.1 0.152
MA0146.1 0.068
MA0147.1 0.448
MA0148.1 0.324
MA0149.1 0.4
MA0150.1 0.00242
MA0152.1 0.269
MA0153.1 1.60913e-7
MA0154.1 9.7804e-4
MA0155.1 0.484
MA0156.1 6.87285e-8
MA0157.1 0.931
MA0159.1 0.00576
MA0160.1 0.131
MA0162.1 0.182
MA0163.1 5.58469e-5
MA0164.1 0.726
MA0258.1 0.00191
MA0259.1 0.26



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs10483
Novel motif P-value
1 0.223
10 0.116
100 0.789
101 0.405
102 0.321
103 0.258
104 0.989
105 0.324
106 0.0874
107 0.362
108 0.835
109 0.0404
11 0.132
110 0.115
111 0.197
112 0.117
113 0.667
114 0.14
115 0.91
116 0.281
117 0.0243
118 0.382
119 0.0711
12 0.401
120 0.646
121 0.341
122 0.753
123 0.97
124 0.89
125 0.0369
126 0.311
127 0.156
128 0.123
129 0.171
13 0.0809
130 0.589
131 0.919
132 0.711
133 0.141
134 0.335
135 0.973
136 0.245
137 0.061
138 0.444
139 0.1
14 0.306
140 0.265
141 0.47
142 0.893
143 0.129
144 0.475
145 0.0932
146 0.612
147 0.971
148 0.189
149 0.175
15 0.0192
150 0.305
151 0.0619
152 0.219
153 0.846
154 0.869
155 0.582
156 0.871
157 0.911
158 0.0931
159 0.995
160 0.573
161 0.257
162 0.587
163 0.704
164 0.0481
165 0.0334
166 0.418
167 0.762
168 0.395
169 9.97624e-4
17 0.242
18 0.205
19 0.174
2 0.746
20 0.614
21 0.0786
22 0.25
23 0.381
24 0.275
25 0.261
26 0.0489
27 0.45
28 0.415
29 0.111
3 0.145
30 0.897
31 0.395
32 0.0926
33 0.361
34 0.347
35 0.439
36 0.146
37 0.117
38 0.368
39 0.911
4 0.983
40 0.103
41 0.344
42 0.313
43 0.136
44 0.318
45 0.444
46 0.177
47 0.181
48 0.256
49 0.192
5 0.0773
50 0.92
51 0.717
52 0.479
53 0.618
54 0.719
55 0.0598
56 0.257
57 0.405
58 0.294
59 0.0213
6 0.678
60 0.157
61 0.366
62 0.0742
63 0.313
64 0.599
65 0.196
66 0.472
67 0.21
68 0.658
69 0.119
7 0.0623
70 0.0603
71 0.0552
72 0.478
73 0.0875
74 0.523
75 0.119
76 0.833
77 0.427
78 0.0127
79 0.512
8 0.0349
80 0.0139
81 0.318
82 0.248
83 0.237
84 0.649
85 0.0456
86 0.313
87 0.187
88 0.807
89 0.201
9 0.277
90 0.79
91 0.269
92 0.43
93 0.281
94 0.0471
95 0.0656
96 0.318
97 0.961
98 0.136
99 0.576



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

library id: CNhs10483


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)
0007023 (adult organism)
0000981 (femur)
0001474 (bone element)
0000479 (tissue)
0011216 (organ system subdivision)
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)
0003608 (hindlimb long bone)
0003826 (upper leg bone)
0008202 (bone of hip region)
0000075 (subdivision of skeletal system)
0004381 (skeleton of limb)
0007273 (pelvic appendage skeleton)
0004765 (skeletal element)
0010912 (subdivision of skeleton)
0004708 (paired limb/fin)
0002101 (limb)
0004709 (pelvic appendage)
0002513 (endochondral bone)
0004375 (bone of free limb or fin)
0010740 (bone of appendage girdle complex)
0002529 (limb segment)
0010363 (endochondral element)
0010538 (paired limb/fin segment)
0002428 (limb bone)
0010742 (bone of pelvic complex)
0002495 (long bone)
0003464 (hindlimb bone)
0003606 (limb long bone)
0005893 (leg bone)
0010317 (germ layer / neural crest derived structure)
0010712 (limb skeleton subdivision)
0010758 (subdivision of organism along appendicular axis)
0010707 (appendage girdle complex)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0000978 (leg)
0002103 (hindlimb)
0000376 (hindlimb stylopod)
0001441 (hindlimb skeleton)
0011249 (appendicular skeletal system)
0000154 (posterior region of body)
0010709 (pelvic complex)
0002091 (appendicular skeleton)
0004288 (skeleton)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011464 (mouse bone- os femoris - adult 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:0003104 (mesenchyme)
UBERON:0005866 (pre-cartilage condensation)
UBERON:0006234 (femur pre-cartilage condensation)
UBERON:0010316 (germ layer / neural crest)
UBERON:0010882 (limb bone pre-cartilage condensation)
UBERON:0010886 (hindlimb bone pre-cartilage condensation)