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|library_id=CNhs10501
|library_id=CNhs10501
|library_id_phase_based=2:CNhs10501
|library_id_phase_based=2:CNhs10501
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/corpora%2520quadrigemina%252c%2520adult.CNhs10501.16-22A4.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/corpora%2520quadrigemina%252c%2520adult.CNhs10501.16-22A4.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/corpora%2520quadrigemina%252c%2520adult.CNhs10501.16-22A4.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/corpora%2520quadrigemina%252c%2520adult.CNhs10501.16-22A4.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/corpora%2520quadrigemina%252c%2520adult.CNhs10501.16-22A4.mm9.nobarcode.rdna.fa.gz
|name=corpora quadrigemina, adult
|name=corpora quadrigemina, adult
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 18:00, 17 May 2017


Name:corpora quadrigemina, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10501
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuecorpora quadrigemina
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005905
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10501 CAGE DRX008944 DRR009818
Accession ID Mm9

Library idBAMCTSS
CNhs10501 DRZ001243 DRZ002626
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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs10501

00
10.774
100
1000
10000
10010.0707
1002-0.0795
10030.0715
10040
10050
10060.677
1007-0.0857
10080
1009-0.0572
101-0.0525
10100
10110.477
10120.204
10130.249
1014-0.0245
1015-0.0749
1016-0.127
10170
10180
10190
1020
10200
10210
10220.0775
10230
10240.103
10250
10260
10270.375
10280
10290.0464
103-0.0861
10300
1031-0.327
10320.43
1033-0.0665
10340
10350
1036-0.179
10370
1038-0.188
10390.219
1040
1040-0.181
10410



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10501

Jaspar motifP-value
MA0002.20.0015
MA0003.10.321
MA0004.10.509
MA0006.10.182
MA0007.10.334
MA0009.10.843
MA0014.10.747
MA0017.13.45883e-6
MA0018.20.0155
MA0019.10.527
MA0024.10.0613
MA0025.15.69827e-4
MA0027.10.0785
MA0028.10.112
MA0029.10.899
MA0030.10.937
MA0031.10.254
MA0035.20.0286
MA0038.10.393
MA0039.20.0254
MA0040.10.377
MA0041.10.0691
MA0042.10.209
MA0043.10.028
MA0046.14.26383e-11
MA0047.22.02389e-4
MA0048.10.032
MA0050.19.55222e-5
MA0051.10.00102
MA0052.10.493
MA0055.10.0083
MA0057.10.349
MA0058.10.501
MA0059.10.152
MA0060.10.931
MA0061.10.0281
MA0062.20.00287
MA0065.22.47898e-6
MA0066.10.0361
MA0067.10.442
MA0068.10.336
MA0069.10.0648
MA0070.10.339
MA0071.10.168
MA0072.10.699
MA0073.10.797
MA0074.10.134
MA0076.10.277
MA0077.10.425
MA0078.10.803
MA0079.20.405
MA0080.28.66167e-10
MA0081.10.231
MA0083.10.00407
MA0084.10.674
MA0087.10.0976
MA0088.10.375
MA0090.10.123
MA0091.10.0926
MA0092.10.159
MA0093.10.58
MA0099.20.00129
MA0100.10.278
MA0101.10.0136
MA0102.20.556
MA0103.10.179
MA0104.20.844
MA0105.10.00674
MA0106.10.0548
MA0107.10.03
MA0108.22.4474e-4
MA0111.10.895
MA0112.20.00109
MA0113.10.363
MA0114.11.09435e-5
MA0115.13.14388e-5
MA0116.10.0669
MA0117.10.964
MA0119.10.13
MA0122.10.959
MA0124.10.509
MA0125.10.0364
MA0131.10.742
MA0135.10.315
MA0136.19.90414e-12
MA0137.20.314
MA0138.29.05945e-5
MA0139.10.601
MA0140.17.76019e-5
MA0141.10.0122
MA0142.10.138
MA0143.10.623
MA0144.10.0859
MA0145.10.144
MA0146.10.0377
MA0147.10.682
MA0148.16.90018e-4
MA0149.10.158
MA0150.10.156
MA0152.10.246
MA0153.15.98758e-12
MA0154.10.0321
MA0155.10.412
MA0156.11.36334e-7
MA0157.10.176
MA0159.10.00323
MA0160.10.0151
MA0162.10.238
MA0163.19.61734e-4
MA0164.10.882
MA0258.10.0184
MA0259.10.829



FANTOM5 phase1 novel unique motifs<b>Summary:</b>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 in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10501

Novel motifP-value
10.234
100.0523
1000.38
1010.827
1020.933
1030.104
1040.962
1050.581
1060.029
1070.109
1080.611
1090.0134
110.0918
1100.0472
1110.281
1120.0155
1130.507
1140.516
1150.686
1160.175
1170.00413
1180.339
1190.237
120.846
1201
1210.673
1220.61
1233.04315e-4
1240.0427
1250.154
1260.0208
1270.244
1280.0408
1290.318
131.74881e-7
1300.136
1310.421
1320.671
1330.745
1340.112
1350.13
1360.0559
1370.703
1380.969
1390.216
140.766
1400.022
1410.972
1420.531
1430.251
1440.734
1452.06086e-4
1460.3
1470.351
1480.723
1490.924
150.198
1500.0702
1510.873
1520.0926
1530.781
1540.726
1550.463
1560.00522
1570.254
1580.389
1590.546
1600.213
1610.166
1620.696
1630.565
1640.0451
1650.175
1660.684
1670.729
1680.648
1690.00435
170.0478
180.97
190.136
20.718
200.0239
210.158
220.174
230.667
240.057
250.771
263.87928e-9
270.399
280.752
290.0396
30.0957
300.845
310.75
320.622
330.168
340.781
350.783
360.269
370.0316
380.528
390.314
40.237
400.104
410.407
420.228
430.139
440.369
450.73
460.0509
470.477
480.337
490.198
50.189
500.264
510.82
520.28
530.402
540.945
550.947
560.499
570.515
580.365
590.111
60.945
600.0333
610.0671
620.237
630.164
640.654
650.406
660.871
670.785
680.891
690.514
70.0193
700.106
710.00219
720.616
730.039
740.871
750.0552
760.374
770.357
780.00224
790.411
80.0618
800.747
810.769
820.349
830.145
840.848
850.24
860.136
870.178
880.475
890.729
90.49
900.148
910.0432
920.34
930.0853
940.773
950.0434
960.496
970.962
980.708
990.521



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs10501


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000955 (brain)
0002259 (corpora quadrigemina)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002950 (regional part of midbrain)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001891 (midbrain)
0002314 (midbrain tectum)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011283 (mouse corpora quadrigemina- adult sample)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006777 (tectal plate)
UBERON:0010316 (germ layer / neural crest)

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