Personal tools

FF:988-6G6: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004897
|DRA_sample_Accession=CAGE@SAMD00004897
|accession_numbers=CAGE;DRX009053;DRR009927;DRZ001352;DRZ002735
|accession_numbers=CAGE;DRX009053;DRR009927;DRZ001352;DRZ002735;DRZ012702;DRZ014085
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000993,UBERON:0000479,UBERON:0005156,UBERON:0004111,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0003100,UBERON:0000474
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000993,UBERON:0000479,UBERON:0005156,UBERON:0004111,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0003100,UBERON:0000474
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=

Revision as of 22:49, 10 August 2017


Name:oviduct, adult pregnant day01
Species:Mouse (Mus musculus)
Library ID:CNhs10500
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueoviduct
dev stage1 day pregnant adult
sexfemale
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  SAMD00004897
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10500 CAGE DRX009053 DRR009927
Accession ID Mm9

Library idBAMCTSS
CNhs10500 DRZ001352 DRZ002735
Accession ID Mm10

Library idBAMCTSS
CNhs10500 DRZ012702 DRZ014085
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

CNhs10500

00
10
100
1000
10000.0663
10010.271
10020.0412
10030.201
10040.648
10050.0436
10060.0189
10070.0667
10080
10090.446
1010.0292
10100
10110.086
10120.0663
10130.118
10140
1015-0.0664
10160.198
10170
10180
10190
1020
10200
10210
10220.124
10230
10240.213
10250.138
10260.232
10270
10280
10290.35
1030.235
10300
10310.587
1032-0.11
10330
10340.0663
10350
1036-0.0283
10370
10380.101
10390.0197
1040
10400.38
10410.0663



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: CNhs10500

Jaspar motifP-value
MA0002.20.948
MA0003.10.084
MA0004.10.623
MA0006.10.178
MA0007.10.814
MA0009.10.83
MA0014.10.758
MA0017.12.55299e-5
MA0018.20.0064
MA0019.10.496
MA0024.10.012
MA0025.10.175
MA0027.10.781
MA0028.10.024
MA0029.10.286
MA0030.10.142
MA0031.10.12
MA0035.20.00186
MA0038.10.296
MA0039.20.0465
MA0040.10.47
MA0041.10.184
MA0042.10.377
MA0043.10.367
MA0046.14.03884e-5
MA0047.20.983
MA0048.10.511
MA0050.13.18734e-8
MA0051.13.71695e-5
MA0052.10.35
MA0055.10.406
MA0057.10.679
MA0058.10.491
MA0059.10.0472
MA0060.10.0155
MA0061.10.627
MA0062.20.0159
MA0065.20.00314
MA0066.10.0105
MA0067.10.62
MA0068.10.501
MA0069.10.52
MA0070.10.772
MA0071.10.00356
MA0072.10.0758
MA0073.10.683
MA0074.10.882
MA0076.10.081
MA0077.10.845
MA0078.10.0155
MA0079.20.0341
MA0080.20.00124
MA0081.10.885
MA0083.14.9262e-6
MA0084.10.186
MA0087.10.299
MA0088.10.271
MA0090.10.641
MA0091.10.23
MA0092.10.682
MA0093.10.715
MA0099.20.692
MA0100.10.643
MA0101.10.754
MA0102.20.993
MA0103.10.712
MA0104.20.019
MA0105.10.107
MA0106.10.663
MA0107.10.18
MA0108.20.176
MA0111.10.903
MA0112.20.594
MA0113.10.331
MA0114.11.01807e-5
MA0115.18.75703e-6
MA0116.10.166
MA0117.10.119
MA0119.10.266
MA0122.10.453
MA0124.10.952
MA0125.10.035
MA0131.10.377
MA0135.10.808
MA0136.10.037
MA0137.20.287
MA0138.20.645
MA0139.10.934
MA0140.10.00178
MA0141.11.32638e-7
MA0142.10.555
MA0143.10.72
MA0144.10.275
MA0145.10.0202
MA0146.10.787
MA0147.10.00778
MA0148.10.954
MA0149.10.0329
MA0150.10.139
MA0152.10.119
MA0153.12.34612e-5
MA0154.10.874
MA0155.10.621
MA0156.10.0129
MA0157.10.0448
MA0159.10.0122
MA0160.17.65576e-4
MA0162.10.68
MA0163.10.0639
MA0164.10.595
MA0258.10.111
MA0259.10.0461



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: CNhs10500

Novel motifP-value
10.169
100.0317
1000.0933
1010.445
1020.997
1030.628
1040.265
1050.851
1060.464
1070.276
1080.416
1090.912
110.172
1100.569
1110.145
1120.38
1130.859
1140.0393
1150.635
1160.425
1170.00107
1180.0401
1190.283
120.817
1200.23
1210.293
1220.653
1230.279
1240.64
1250.386
1260.771
1270.0691
1280.969
1290.793
130.894
1300.0392
1310.692
1320.721
1330.33
1340.531
1350.223
1360.44
1370.381
1380.0287
1390.688
140.679
1400.453
1410.592
1420.344
1430.156
1440.644
1450.621
1460.366
1470.364
1480.311
1490.094
150.857
1500.805
1510.829
1520.0562
1530.741
1540.948
1550.893
1560.246
1570.794
1580.78
1590.139
1600.8
1610.618
1620.717
1630.205
1640.649
1650.802
1660.00105
1670.0606
1680.308
1690.0742
170.57
180.0126
190.165
20.0379
200.18
210.744
220.48
230.595
240.25
250.131
260.861
270.429
280.538
290.0734
30.337
300.239
310.588
320.19
330.388
340.696
350.0178
360.015
370.863
380.673
390.569
40.819
400.108
410.122
420.651
430.336
440.0875
450.208
460.435
470.853
480.559
490.186
50.262
500.436
510.938
520.255
530.159
540.656
550.864
560.684
570.215
580.623
590.934
60.413
600.633
610.602
620.146
630.851
640.206
650.982
660.349
670.427
680.347
690.413
70.531
700.191
710.0422
720.579
730.923
740.84
750.0383
760.165
770.896
780.00427
790.691
80.042
800.178
810.481
820.908
830.908
840.99
850.834
860.92
870.438
880.668
890.918
90.505
900.0166
910.554
920.635
930.472
940.0987
950.12
960.0449
970.232
980.659
990.284



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: CNhs10500


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)
0000993 (oviduct)
0000479 (tissue)
0005156 (reproductive structure)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0003100 (female organism)
0000474 (female reproductive system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000317 (mouse pregnant tissue sample)
0000318 (mouse pregnant day 1 sample)
0011442 (mouse oviduct- adult pregnant day01 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:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:988-6G6&oldid=4345948"