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FF:1387-42A2

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Name:epididymis and seminiferous tubule, neonate N30
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueepididymis and seminiferous tubule
dev stage30 days neonate
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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs11199

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.337
1001 0.209
1002 0.0242
1003 --0.00968
1004 0.0509
1005 0.229
1006 0.275
1007 0.0472
1008 0
1009 0.269
101 --0.0484
1010 0
1011 0.024
1012 0.0509
1013 0.11
1014 0
1015 --0.145
1016 --0.107
1017 0
1018 0.0637
1019 0.0509
102 0
1020 0
1021 0.138
1022 0.244
1023 0.0509
1024 0.12
1025 0
1026 0.516
1027 0.0509
1028 0.0509
1029 0.124
103 1.021
1030 0.21
1031 0.0357
1032 0.0318
1033 0.0342
1034 0.124
1035 0.0187
1036 0.00302
1037 0.0509
1038 --0.0447
1039 0.0332
104 0
1040 0.0783
1041 0.708



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: CNhs11199

Jaspar motif P-value
MA0002.2 1.52627e-7
MA0003.1 0.00872
MA0004.1 0.218
MA0006.1 0.0905
MA0007.1 0.0272
MA0009.1 0.785
MA0014.1 0.705
MA0017.1 0.806
MA0018.2 1.45093e-5
MA0019.1 0.0579
MA0024.1 0.898
MA0025.1 0.297
MA0027.1 0.41
MA0028.1 0.0467
MA0029.1 0.492
MA0030.1 0.621
MA0031.1 0.591
MA0035.2 0.0352
MA0038.1 0.656
MA0039.2 0.0401
MA0040.1 0.0854
MA0041.1 0.354
MA0042.1 0.529
MA0043.1 1.73304e-5
MA0046.1 0.0021
MA0047.2 0.865
MA0048.1 0.459
MA0050.1 5.56981e-4
MA0051.1 0.0027
MA0052.1 4.41334e-12
MA0055.1 0.442
MA0057.1 0.321
MA0058.1 0.167
MA0059.1 0.179
MA0060.1 0.676
MA0061.1 0.215
MA0062.2 0.0301
MA0065.2 0.24
MA0066.1 0.662
MA0067.1 0.403
MA0068.1 0.00875
MA0069.1 0.671
MA0070.1 0.811
MA0071.1 0.982
MA0072.1 0.0629
MA0073.1 0.836
MA0074.1 0.935
MA0076.1 0.0205
MA0077.1 0.162
MA0078.1 0.0251
MA0079.2 0.972
MA0080.2 3.23998e-10
MA0081.1 0.141
MA0083.1 6.89132e-4
MA0084.1 0.863
MA0087.1 0.61
MA0088.1 0.883
MA0090.1 0.784
MA0091.1 0.241
MA0092.1 0.46
MA0093.1 0.197
MA0099.2 0.817
MA0100.1 0.814
MA0101.1 0.847
MA0102.2 0.137
MA0103.1 0.871
MA0104.2 0.0952
MA0105.1 0.11
MA0106.1 0.494
MA0107.1 0.735
MA0108.2 0.031
MA0111.1 0.763
MA0112.2 5.6601e-5
MA0113.1 0.00825
MA0114.1 0.187
MA0115.1 0.0233
MA0116.1 0.0469
MA0117.1 0.856
MA0119.1 0.0468
MA0122.1 0.411
MA0124.1 0.867
MA0125.1 0.054
MA0131.1 0.607
MA0135.1 0.922
MA0136.1 3.10583e-6
MA0137.2 0.0467
MA0138.2 0.94
MA0139.1 0.34
MA0140.1 2.30253e-11
MA0141.1 0.9
MA0142.1 0.696
MA0143.1 0.371
MA0144.1 0.903
MA0145.1 0.0615
MA0146.1 0.251
MA0147.1 0.106
MA0148.1 0.966
MA0149.1 0.566
MA0150.1 0.281
MA0152.1 0.98
MA0153.1 9.72368e-4
MA0154.1 0.00355
MA0155.1 0.304
MA0156.1 2.62969e-4
MA0157.1 0.494
MA0159.1 0.312
MA0160.1 0.859
MA0162.1 0.519
MA0163.1 0.00294
MA0164.1 0.287
MA0258.1 0.0068
MA0259.1 0.0533



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: CNhs11199

Novel motif P-value
1 0.537
10 0.589
100 0.982
101 0.84
102 0.827
103 0.334
104 0.295
105 0.425
106 0.0078
107 0.063
108 0.414
109 0.133
11 0.487
110 0.303
111 0.682
112 0.108
113 0.432
114 0.799
115 0.738
116 0.363
117 0.691
118 0.75
119 0.0686
12 0.353
120 0.557
121 0.421
122 0.348
123 0.515
124 0.138
125 0.238
126 0.561
127 0.76
128 0.0229
129 0.559
13 0.00665
130 0.0508
131 0.584
132 0.974
133 0.356
134 0.236
135 0.3
136 0.63
137 0.0274
138 0.441
139 0.879
14 0.332
140 0.511
141 0.825
142 0.108
143 0.155
144 0.38
145 0.197
146 0.307
147 0.88
148 0.109
149 0.00677
15 0.038
150 0.409
151 0.146
152 0.0733
153 0.69
154 0.826
155 0.965
156 0.0213
157 0.184
158 0.922
159 0.581
160 0.288
161 0.509
162 0.618
163 0.323
164 0.266
165 0.00137
166 0.0881
167 0.0874
168 0.169
169 9.79221e-4
17 0.236
18 0.543
19 0.0132
2 0.13
20 0.64
21 0.0739
22 0.139
23 0.159
24 0.0626
25 0.776
26 0.0152
27 0.439
28 0.671
29 0.427
3 0.242
30 0.521
31 0.536
32 0.00282
33 0.974
34 0.164
35 0.502
36 0.457
37 0.0763
38 0.409
39 0.0873
4 0.594
40 0.143
41 0.079
42 0.568
43 0.238
44 0.492
45 0.23
46 0.263
47 0.477
48 0.625
49 0.477
5 0.213
50 0.219
51 0.468
52 0.119
53 0.125
54 0.489
55 0.101
56 0.632
57 0.672
58 0.268
59 0.0118
6 0.0792
60 0.0466
61 0.795
62 0.151
63 0.106
64 0.882
65 0.292
66 0.823
67 0.554
68 0.987
69 0.00625
7 0.099
70 0.417
71 0.0977
72 0.649
73 0.12
74 0.315
75 0.455
76 0.423
77 0.398
78 0.0764
79 0.825
8 0.593
80 0.0664
81 0.335
82 0.188
83 0.28
84 0.639
85 0.0324
86 0.446
87 0.277
88 0.981
89 0.471
9 0.237
90 0.29
91 0.0326
92 0.326
93 0.545
94 0.169
95 0.259
96 0.418
97 0.429
98 0.523
99 0.477



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: CNhs11199


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)
0000473 (testis)
0000991 (gonad)
0001301 (epididymis)
0001343 (seminiferous tubule of testis)
0000479 (tissue)
0000058 (duct)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0005904 (duct of male reproductive system)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0004175 (internal genitalia)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive system)
0006947 (male genital duct)
0004054 (internal male genitalia)

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)
0011471 (mouse epididymis and seminiferous tubule- 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:0004871 (somatic layer of lateral plate mesoderm)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0007297 (presumptive pronephric mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)