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|library_id=CNhs11205
|library_id=CNhs11205
|library_id_phase_based=2:CNhs11205
|library_id_phase_based=2:CNhs11205
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520neonate%2520N02.CNhs11205.1551-44G8.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520neonate%2520N02.CNhs11205.1551-44G8.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520neonate%2520N02.CNhs11205.1551-44G8.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520neonate%2520N02.CNhs11205.1551-44G8.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520neonate%2520N02.CNhs11205.1551-44G8.mm9.nobarcode.rdna.fa.gz
|name=eyeball, neonate N02
|name=eyeball, neonate N02
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 17:59, 17 May 2017


Name:eyeball, neonate N02
Species:Mouse (Mus musculus)
Library ID:CNhs11205
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueeyeball
dev stage2 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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005344
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11205 CAGE DRX008961 DRR009835
Accession ID Mm9

Library idBAMCTSS
CNhs11205 DRZ001260 DRZ002643
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

CNhs11205

00
10.171
100
1000.138
10000.0567
10010.197
10020.274
10030.0359
10040.123
10050
10060.255
10070.0605
10080
10090.0059
1010.0024
10100
10110.107
10120.108
1013-0.121
10140.167
10150.164
10160.223
10170
10180.0389
10190
1020
10200
10210.0896
10220.0324
10230
10245.312076e-4
10250
10260.0746
10270.924
10280
10290.209
1030.38
10300
10310.278
10320.0575
10330.0104
10340
10350.0389
1036-0.106
10370
10380.121
1039-0.135
1040
1040-0.073
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: CNhs11205

Jaspar motifP-value
MA0002.21.4735e-5
MA0003.10.235
MA0004.10.351
MA0006.10.289
MA0007.10.211
MA0009.10.147
MA0014.10.18
MA0017.11.19383e-7
MA0018.20.203
MA0019.10.548
MA0024.10.0311
MA0025.10.102
MA0027.10.218
MA0028.10.222
MA0029.10.462
MA0030.10.884
MA0031.10.244
MA0035.20.00583
MA0038.19.23695e-4
MA0039.20.0539
MA0040.10.101
MA0041.10.453
MA0042.10.909
MA0043.10.821
MA0046.11.19065e-21
MA0047.21.26985e-4
MA0048.10.483
MA0050.12.33294e-4
MA0051.10.00434
MA0052.10.236
MA0055.10.723
MA0057.10.158
MA0058.10.345
MA0059.10.266
MA0060.15.65431e-9
MA0061.10.0223
MA0062.20.00333
MA0065.25.12979e-7
MA0066.10.179
MA0067.10.948
MA0068.10.0333
MA0069.10.0178
MA0070.10.533
MA0071.10.952
MA0072.10.0236
MA0073.10.608
MA0074.10.363
MA0076.10.588
MA0077.10.0166
MA0078.10.738
MA0079.20.541
MA0080.21.17088e-12
MA0081.10.039
MA0083.10.739
MA0084.10.0758
MA0087.10.449
MA0088.10.0829
MA0090.10.628
MA0091.10.0831
MA0092.10.418
MA0093.10.37
MA0099.22.10329e-5
MA0100.10.56
MA0101.10.0465
MA0102.20.253
MA0103.10.00345
MA0104.20.827
MA0105.10.00163
MA0106.10.239
MA0107.10.0525
MA0108.20.0013
MA0111.10.961
MA0112.23.89883e-4
MA0113.10.148
MA0114.11.44287e-6
MA0115.15.81015e-6
MA0116.10.00789
MA0117.10.683
MA0119.10.0811
MA0122.10.873
MA0124.10.537
MA0125.14.57794e-4
MA0131.10.724
MA0135.10.802
MA0136.12.99219e-15
MA0137.20.00322
MA0138.20.355
MA0139.10.0752
MA0140.15.25301e-4
MA0141.15.49875e-4
MA0142.10.351
MA0143.10.126
MA0144.10.0117
MA0145.10.0613
MA0146.10.0762
MA0147.10.593
MA0148.12.67633e-4
MA0149.10.0255
MA0150.10.0411
MA0152.10.339
MA0153.11.92566e-25
MA0154.10.00487
MA0155.10.943
MA0156.11.65215e-7
MA0157.10.0992
MA0159.10.00822
MA0160.10.00448
MA0162.10.351
MA0163.13.44755e-4
MA0164.10.802
MA0258.10.0166
MA0259.10.897



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: CNhs11205

Novel motifP-value
10.113
100.0816
1000.824
1010.556
1020.641
1030.0109
1040.63
1050.573
1060.0756
1070.21
1080.906
1090.0085
110.0451
1100.0931
1115.23853e-4
1120.00289
1130.92
1140.0214
1150.98
1160.275
1170.0141
1180.295
1190.103
120.304
1200.213
1210.598
1220.811
1230.547
1240.703
1250.0535
1260.167
1270.0612
1280.126
1290.311
130.00279
1300.97
1310.473
1320.577
1330.684
1340.584
1350.23
1360.0981
1370.329
1380.179
1390.0333
140.911
1400.0927
1410.0257
1420.718
1430.149
1440.786
1450.05
1460.447
1470.717
1480.332
1490.183
150.0626
1500.241
1510.393
1520.049
1530.639
1540.977
1550.187
1560.617
1570.68
1580.18
1590.417
1600.344
1610.195
1620.826
1630.582
1640.00458
1650.00809
1660.705
1670.711
1680.762
1690.00368
170.0452
180.477
190.301
20.582
200.496
210.232
220.242
230.387
240.0773
250.482
260.012
270.447
280.312
290.0437
30.0587
300.9
310.535
320.303
330.239
340.761
350.599
360.269
370.0209
380.262
390.389
40.604
400.307
410.364
420.231
430.179
440.109
450.52
460.127
470.0848
480.0826
490.162
50.132
500.696
510.582
520.353
530.866
540.685
550.466
560.312
570.647
580.211
590.033
60.608
600.0393
610.244
620.0799
630.0803
640.496
650.157
660.563
670.969
680.131
690.984
70.0674
700.00804
710.0135
720.279
730.0184
740.285
750.0241
760.59
770.166
780.0313
790.0908
80.0362
800.332
810.27
820.00952
830.51
840.168
850.0466
860.117
870.178
880.466
890.0824
90.613
900.0875
910.741
920.063
930.238
940.311
950.0213
960.451
970.923
980.372
990.504



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: CNhs11205


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)
0000970 (eye)
0000019 (camera-type eye)
0000033 (head)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0000047 (simple eye)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0001032 (sensory system)
0010317 (germ layer / neural crest derived structure)
0004088 (ocular region)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002104 (visual system)
0004456 (entire sense organ system)
0001456 (face)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000307 (mouse neonate N2 sample)
0011281 (mouse eyeball- neonate N02 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:0003056 (pre-chordal neural plate)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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