Personal tools

FF:1265-44F5: 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@DRS008935
|DRA_sample_Accession=CAGE@SAMD00005078
|accession_numbers=CAGE;DRX009072;DRR009946;DRZ001371;DRZ002754
|accession_numbers=CAGE;DRX009072;DRR009946;DRZ001371;DRZ002754
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0000007,UBERON:0001894,UBERON:0000479,UBERON:0004121,UBERON:0003296,UBERON:0010133,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0002616,UBERON:0002780,UBERON:0002530,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001890,UBERON:0000949
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0000007,UBERON:0001894,UBERON:0000479,UBERON:0004121,UBERON:0003296,UBERON:0010133,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0002616,UBERON:0002780,UBERON:0002530,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001890,UBERON:0000949

Revision as of 21:25, 31 July 2014


Name:pituitary gland, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs11039
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepituitary gland
dev stage17 days embryo
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  SAMD00005078
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11039 CAGE DRX009072 DRR009946
Accession ID Mm9

Library idBAMCTSS
CNhs11039 DRZ001371 DRZ002754
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs11039

00
10.174
100
1000.0662
1000-0.0024
10010
10020.197
10030.0914
10040.328
10050
10060.13
10070.0213
10080
10090.0549
101-0.0628
10100
10110.016
10120.0662
10130.069
10140.402
10150.179
10160.236
10170
10180
10190
1020
10200
10210
10220.0176
10230
10240.142
10250.00503
10260
10270.213
10280
10290.105
1030.473
10300
10310.492
10320.0203
10330.124
10340
10350
10360.0313
10370
10380.00635
1039-0.0425
1040
10400.106
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: CNhs11039

Jaspar motifP-value
MA0002.22.98391e-7
MA0003.10.177
MA0004.10.506
MA0006.10.501
MA0007.10.543
MA0009.10.805
MA0014.10.535
MA0017.11.98568e-9
MA0018.20.044
MA0019.10.697
MA0024.10.312
MA0025.10.454
MA0027.10.804
MA0028.10.777
MA0029.10.967
MA0030.10.869
MA0031.10.852
MA0035.20.0013
MA0038.10.183
MA0039.20.368
MA0040.10.337
MA0041.10.37
MA0042.10.735
MA0043.10.0664
MA0046.11.12868e-25
MA0047.20.00289
MA0048.10.249
MA0050.10.0426
MA0051.10.0711
MA0052.11.50423e-6
MA0055.10.781
MA0057.10.156
MA0058.10.468
MA0059.10.178
MA0060.11.38505e-4
MA0061.10.0287
MA0062.20.177
MA0065.21.88112e-6
MA0066.10.00528
MA0067.10.724
MA0068.10.0623
MA0069.10.163
MA0070.10.929
MA0071.10.016
MA0072.10.0358
MA0073.10.713
MA0074.10.202
MA0076.10.66
MA0077.10.524
MA0078.10.139
MA0079.20.173
MA0080.23.30083e-9
MA0081.10.192
MA0083.10.103
MA0084.10.377
MA0087.10.859
MA0088.10.303
MA0090.10.114
MA0091.10.918
MA0092.10.558
MA0093.10.586
MA0099.24.26099e-5
MA0100.10.51
MA0101.10.0547
MA0102.20.926
MA0103.10.29
MA0104.20.465
MA0105.10.00188
MA0106.10.144
MA0107.10.0338
MA0108.20.49
MA0111.10.781
MA0112.22.22011e-7
MA0113.10.951
MA0114.15.15379e-8
MA0115.12.84069e-7
MA0116.10.0106
MA0117.10.805
MA0119.10.0786
MA0122.10.999
MA0124.10.792
MA0125.10.0375
MA0131.10.566
MA0135.10.569
MA0136.12.27311e-8
MA0137.20.0713
MA0138.20.945
MA0139.10.16
MA0140.17.87287e-4
MA0141.15.36801e-4
MA0142.10.8
MA0143.10.92
MA0144.10.102
MA0145.10.218
MA0146.10.091
MA0147.10.395
MA0148.10.00153
MA0149.10.00882
MA0150.12.83872e-4
MA0152.10.498
MA0153.14.02288e-22
MA0154.10.0125
MA0155.10.922
MA0156.10.00228
MA0157.10.871
MA0159.17.62718e-4
MA0160.10.00165
MA0162.10.298
MA0163.11.6014e-4
MA0164.10.624
MA0258.13.24227e-5
MA0259.10.814



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: CNhs11039

Novel motifP-value
10.0623
100.0638
1000.748
1010.585
1020.992
1030.149
1040.522
1050.593
1060.0129
1070.0583
1080.837
1090.111
110.117
1100.0641
1110.0127
1120.0416
1130.755
1140.0572
1150.664
1160.379
1170.013
1180.415
1190.0839
120.652
1200.694
1210.42
1220.488
1230.875
1240.853
1250.242
1260.131
1270.0561
1280.0265
1290.144
130.00703
1300.598
1310.935
1320.626
1330.497
1340.722
1350.142
1360.929
1370.8
1380.535
1390.0345
140.614
1400.0185
1410.623
1420.288
1430.85
1440.636
1450.113
1460.447
1470.999
1480.584
1490.441
150.0655
1500.171
1510.345
1520.2
1530.993
1540.715
1550.585
1561.90575e-5
1570.735
1580.205
1590.925
1600.538
1610.557
1620.893
1630.0825
1640.0451
1650.0562
1660.49
1670.0991
1680.657
1695.16478e-4
170.143
180.47
190.157
20.958
200.598
210.835
220.247
230.372
240.318
250.364
260.012
270.6
280.425
290.0931
30.165
300.981
310.65
320.491
330.266
340.777
350.381
360.234
370.0525
380.469
390.634
40.363
400.354
410.055
420.425
430.0869
440.0913
450.51
460.0738
470.26
480.0921
490.0951
50.0551
500.844
510.507
520.26
530.973
540.441
550.283
560.545
570.435
580.318
590.081
60.725
600.0284
610.261
620.0734
630.106
640.428
650.22
660.768
670.69
680.1
690.662
70.0625
700.0217
710.0265
720.378
730.0789
740.47
750.0648
760.837
770.238
780.00575
790.769
80.0445
800.183
810.489
820.174
830.293
840.212
850.0447
860.154
870.549
880.488
890.232
90.56
900.252
910.263
920.192
930.0274
940.226
950.163
960.197
970.787
980.414
990.629



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: CNhs11039


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)
0000922 (embryo)
0000955 (brain)
0000007 (pituitary gland)
0001894 (diencephalon)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0003296 (gland of diencephalon)
0010133 (neuroendocrine gland)
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)
0002368 (endocrine gland)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001890 (forebrain)
0000949 (endocrine system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000300 (mouse embryonic day 17 sample)
0011519 (mouse pituitary gland- embryo E17 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: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:1265-44F5&oldid=3271457"