Personal tools

FF:1299-22I4: 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@SAMD00005795
|DRA_sample_Accession=CAGE@SAMD00005795
|accession_numbers=CAGE;DRX009052;DRR009926;DRZ001351;DRZ002734
|accession_numbers=CAGE;DRX009052;DRR009926;DRZ001351;DRZ002734;DRZ012701;DRZ014084
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000992,UBERON:0000991,UBERON:0003134,UBERON:0000479,UBERON:0005156,UBERON:0000466,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003133,UBERON:0002323,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0003100,UBERON:0000474
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000992,UBERON:0000991,UBERON:0003134,UBERON:0000479,UBERON:0005156,UBERON:0000466,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003133,UBERON:0002323,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0003100,UBERON:0000474
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=

Revision as of 21:58, 10 August 2017


Name:ovary, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11217
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueovary
dev stage0 day neonate
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  SAMD00005795
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11217 CAGE DRX009052 DRR009926
Accession ID Mm9

Library idBAMCTSS
CNhs11217 DRZ001351 DRZ002734
Accession ID Mm10

Library idBAMCTSS
CNhs11217 DRZ012701 DRZ014084
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

CNhs11217

00
10
100
1000
10000.0499
10010.0547
10020.537
10030.179
10040.527
10050
10060.0655
10070.136
10080
10090.347
1010.0293
10100
1011-0.042
10120.015
1013-0.141
10140.362
10150.172
10160.391
10170
10180
10190
1020
10200
10210
10220
10230
10240.0829
10250.173
10260.122
10270
10280
10290.0828
1030.536
10300
10310.686
1032-0.0263
10330
10340.0655
10350
10360.046
10370
10380.127
1039-0.126
1040
10400.345
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: CNhs11217

Jaspar motifP-value
MA0002.23.0144e-4
MA0003.10.66
MA0004.10.814
MA0006.10.859
MA0007.10.507
MA0009.10.209
MA0014.10.402
MA0017.12.86546e-5
MA0018.20.203
MA0019.10.691
MA0024.10.00167
MA0025.10.0877
MA0027.10.197
MA0028.10.344
MA0029.10.704
MA0030.10.686
MA0031.10.914
MA0035.20.0603
MA0038.10.48
MA0039.20.803
MA0040.10.388
MA0041.10.414
MA0042.10.562
MA0043.10.707
MA0046.15.84093e-10
MA0047.20.072
MA0048.10.585
MA0050.10.855
MA0051.10.665
MA0052.10.707
MA0055.10.207
MA0057.10.394
MA0058.10.729
MA0059.10.201
MA0060.10.0247
MA0061.10.165
MA0062.20.0475
MA0065.20.00103
MA0066.10.0176
MA0067.10.473
MA0068.10.354
MA0069.10.479
MA0070.10.64
MA0071.10.034
MA0072.10.016
MA0073.10.928
MA0074.10.849
MA0076.10.664
MA0077.10.577
MA0078.10.0776
MA0079.20.0716
MA0080.21.25073e-5
MA0081.10.164
MA0083.10.0648
MA0084.10.424
MA0087.10.378
MA0088.10.074
MA0090.10.379
MA0091.10.306
MA0092.10.689
MA0093.10.819
MA0099.20.0326
MA0100.10.576
MA0101.10.595
MA0102.20.681
MA0103.10.00526
MA0104.20.348
MA0105.11.91924e-5
MA0106.10.437
MA0107.10.577
MA0108.20.862
MA0111.10.56
MA0112.27.61412e-5
MA0113.10.74
MA0114.12.17801e-4
MA0115.13.79332e-4
MA0116.10.00108
MA0117.10.164
MA0119.10.259
MA0122.10.657
MA0124.10.14
MA0125.10.945
MA0131.10.441
MA0135.10.781
MA0136.12.31749e-6
MA0137.20.187
MA0138.20.00978
MA0139.10.0188
MA0140.10.178
MA0141.10.00191
MA0142.10.00672
MA0143.10.895
MA0144.10.378
MA0145.10.141
MA0146.10.965
MA0147.10.286
MA0148.10.0131
MA0149.10.011
MA0150.10.00155
MA0152.10.182
MA0153.16.86507e-9
MA0154.10.0151
MA0155.10.641
MA0156.10.0368
MA0157.10.813
MA0159.10.00389
MA0160.10.00726
MA0162.10.382
MA0163.10.0428
MA0164.10.725
MA0258.16.30243e-4
MA0259.10.938



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: CNhs11217

Novel motifP-value
10.0385
100.081
1000.884
1010.585
1020.727
1030.132
1040.557
1050.594
1060.127
1070.884
1080.727
1090.221
110.117
1100.319
1110.0284
1120.376
1130.837
1140.0111
1150.392
1160.97
1170.0373
1180.614
1190.0893
120.524
1200.278
1210.643
1220.897
1230.204
1240.114
1250.259
1260.503
1270.0747
1280.0484
1290.381
130.374
1300.345
1310.433
1320.809
1330.444
1340.976
1350.213
1360.536
1370.898
1380.172
1390.0395
140.434
1400.853
1410.205
1420.755
1430.0894
1440.2
1450.619
1460.561
1470.573
1480.638
1490.491
150.0603
1500.984
1510.112
1520.886
1530.571
1540.924
1550.76
1560.00122
1570.306
1580.121
1590.988
1600.906
1610.301
1620.915
1630.151
1640.235
1650.153
1660.0899
1670.278
1680.494
1690.104
170.268
180.0947
190.916
20.719
200.746
210.887
220.766
230.268
240.732
250.151
260.514
270.501
280.239
290.138
30.131
300.868
310.444
320.762
330.938
340.994
350.0152
360.0179
370.159
380.622
390.755
40.675
400.231
410.0542
420.326
430.14
440.0546
450.981
460.176
470.089
480.143
490.0631
50.13
500.574
510.715
520.814
530.989
540.412
550.399
560.211
570.367
580.259
590.414
60.947
600.354
610.909
620.0439
630.278
640.362
650.183
660.929
670.934
680.0452
690.471
70.295
700.00301
710.0913
720.469
730.237
740.877
750.0332
760.956
770.335
780.161
790.89
80.0236
800.155
810.334
820.181
830.358
840.494
850.0346
860.13
870.313
880.83
890.203
90.806
900.0162
910.646
920.208
930.946
940.132
950.182
960.106
970.865
980.234
990.99



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: CNhs11217


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)
0000992 (female gonad)
0000991 (gonad)
0003134 (female reproductive organ)
0000479 (tissue)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011510 (mouse ovary, neonate N00 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:0009117 (indifferent gonad)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0005564 (gonad primordium)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:1299-22I4&oldid=4344763"