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FF:10003-101A7

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Name:SABiosciences XpressRef Mouse Universal Total RNA, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs10611
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuewhole body
dev stageUNDEFINED
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companySABiosciences
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA705103
catalog numberCat:GA-005
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005255
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10611 CAGE DRX008924 DRR009798
Accession ID Mm9

Library idBAMCTSS
CNhs10611 DRZ001223 DRZ002606
Accession ID Mm10

Library idBAMCTSS
CNhs10611 DRZ012573 DRZ013956
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

CNhs10611

MCL coexpression id Coexpression dpi cluster scores median value
0 0.153
1 0.0571
10 0.0571
100 0
1000 0.744
1001 0.11
1002 --0.0334
1003 0.131
1004 0
1005 0.131
1006 0.596
1007 --0.145
1008 1.177
1009 0.0974
101 --0.0481
1010 0
1011 0.206
1012 0
1013 0.22
1014 --0.0874
1015 --0.193
1016 --0.272
1017 0
1018 0.194
1019 0.297
102 0
1020 0
1021 0
1022 0.741
1023 0
1024 0.144
1025 0.236
1026 0.194
1027 0
1028 0
1029 --0.0685
103 0.123
1030 0.108
1031 --0.3
1032 0.174
1033 --0.0737
1034 0.269
1035 0
1036 --0.367
1037 0.108
1038 --0.11
1039 0.502
104 0
1040 --0.158
1041 0.451



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: CNhs10611

P-value
0.0556
0.00892
0.852
0.279
0.523
0.162
0.866
2.24196e-10
0.978
0.903
0.0125
0.00948
0.532
0.0337
0.446
0.0262
0.0268
5.46371e-4
0.901
0.121
0.0885
0.264
0.565
0.378
1.99647e-57
6.87632e-4
0.332
0.344
0.911
4.35728e-7
0.382
0.255
0.728
0.795
0.533
0.806
1.50984e-4
2.17268e-10
0.0906
0.353
0.683
0.461
0.966
0.0398
0.268
0.848
0.564
0.00812
0.832
0.0537
0.572
0.165
0.103
0.217
0.735
0.922
0.398
0.112
0.83
0.338
0.742
0.509
0.0415
0.296
0.955
0.0203
0.96
0.157
0.863
0.228
8.75735e-18
0.413
3.11231e-6
0.393
3.83557e-10
6.07712e-7
0.0351
0.883
0.0557
0.636
0.488
0.433
0.429
0.624
0.0191
0.334
1.7811e-4
0.153
0.0411
2.92985e-4
0.525
0.0883
0.638
0.0186
0.121
0.871
0.00108
0.182
0.0598
0.138
1.08698e-33
0.0101
0.206
0.00361
0.13
0.00464
1.75553e-5
0.117
0.001
0.746
1.009e-4
0.304



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: CNhs10611

P-value
0.177
0.534
0.724
0.138
0.797
0.27
0.368
0.475
0.0836
0.147
0.989
0.0937
0.128
0.228
0.255
0.0753
0.598
0.08
0.628
0.0657
0.76
0.708
0.0623
0.599
0.611
0.0711
0.447
0.743
0.78
0.741
0.437
0.865
0.167
0.681
0.14
0.639
0.217
0.588
0.556
0.916
0.507
0.211
0.784
0.989
0.0577
0.314
0.966
0.43
0.991
0.926
0.847
0.276
0.16
0.874
0.96
0.268
0.318
0.448
0.303
0.12
0.596
0.647
0.873
1.16178e-4
0.607
0.351
0.476
0.405
0.717
0.441
0.842
0.606
0.199
0.477
0.303
0.239
0.00211
0.129
0.98
0.0768
0.34
0.547
0.66
0.147
0.153
0.0518
0.427
0.308
0.53
0.389
0.521
0.213
0.32
0.27
0.0213
0.64
0.302
0.527
0.436
0.133
0.41
0.388
0.601
0.0997
0.0295
0.512
0.206
0.0191
0.248
0.234
0.148
0.186
0.27
0.481
0.624
0.553
0.2
0.662
0.401
0.951
0.495
0.975
0.237
0.0169
0.663
0.15
0.853
0.115
0.105
0.437
0.22
0.604
0.589
0.478
0.514
0.271
0.0449
0.205
0.273
0.178
0.409
0.251
0.369
0.0615
0.558
0.366
0.018
0.265
0.435
0.045
0.232
0.104
0.0185
0.31
0.0196
0.36
0.0467
0.541
0.401
0.249
0.283
0.689
0.855
0.211
0.404
0.121
0.421
0.101



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: CNhs10611


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
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000343 (control treatment 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

NA