Personal tools

FF:755-23A5: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 9: Line 9:
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=1
|datafreeze_phase=1
|datafreeze_phase=1
|def=
|def=
Line 44: Line 45:
|is_obsolete=
|is_obsolete=
|library_id=CNhs11098
|library_id=CNhs11098
|library_id_phase_based=1:CNhs11098
|name=intestine, neonate N10
|name=intestine, neonate N10
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 12:06, 18 June 2014


Name:intestine, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11098
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestine
dev stage10 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  DRS008863
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11098 CAGE DRX009000 DRR009874
Accession ID Mm9

Library idBAMCTSS
CNhs11098 DRZ001299 DRZ002682
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

CNhs11098

00
10
100
1000
10000.0774
10010.024
10020.149
1003-0.025
10040
10050.2
10060
1007-0.00978
10080.548
10090.18
101-0.0687
10100.0774
1011-0.0357
10120
10130.201
10140.107
1015-0.146
1016-0.0493
10170
10180.374
10190
1020
10200
1021-0.0487
10220.00697
10230
10240.156
10250.784
10260
10270
10280
10290.348
1030.15
10300
10310.0506
10320.325
1033-0.0665
10340.0156
10350
1036-0.102
10370
10380.0514
10390.018
1040.143
1040-0.0438
10410.0774



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: CNhs11098

Jaspar motifP-value
MA0002.20.0861
MA0003.10.121
MA0004.10.843
MA0006.10.0266
MA0007.10.415
MA0009.10.463
MA0014.10.799
MA0017.18.48901e-28
MA0018.20.00228
MA0019.10.212
MA0024.10.0187
MA0025.10.336
MA0027.10.193
MA0028.10.133
MA0029.10.789
MA0030.10.319
MA0031.10.218
MA0035.22.88729e-6
MA0038.10.814
MA0039.21.19223e-4
MA0040.10.0606
MA0041.10.37
MA0042.10.911
MA0043.10.00215
MA0046.13.88361e-75
MA0047.23.47291e-5
MA0048.10.722
MA0050.15.69282e-8
MA0051.17.40381e-6
MA0052.10.00146
MA0055.10.184
MA0057.10.118
MA0058.10.595
MA0059.10.69
MA0060.10.0222
MA0061.10.559
MA0062.20.0726
MA0065.29.17153e-12
MA0066.10.319
MA0067.10.41
MA0068.10.785
MA0069.10.0303
MA0070.10.117
MA0071.10.736
MA0072.10.665
MA0073.10.739
MA0074.10.181
MA0076.10.0661
MA0077.10.115
MA0078.10.113
MA0079.20.235
MA0080.20.00357
MA0081.10.14
MA0083.10.134
MA0084.10.646
MA0087.10.987
MA0088.10.948
MA0090.10.376
MA0091.10.561
MA0092.10.172
MA0093.10.745
MA0099.20.0118
MA0100.10.00708
MA0101.10.584
MA0102.20.601
MA0103.11.55215e-5
MA0104.20.0716
MA0105.10.73
MA0106.10.815
MA0107.10.653
MA0108.20.00599
MA0111.10.51
MA0112.24.64534e-4
MA0113.10.621
MA0114.13.83109e-33
MA0115.13.47783e-8
MA0116.10.691
MA0117.10.993
MA0119.10.0673
MA0122.10.88
MA0124.10.208
MA0125.10.613
MA0131.10.329
MA0135.10.029
MA0136.10.053
MA0137.20.588
MA0138.20.711
MA0139.10.0268
MA0140.10.037
MA0141.10.0215
MA0142.10.062
MA0143.10.0352
MA0144.10.0431
MA0145.10.00596
MA0146.10.122
MA0147.10.0366
MA0148.16.41801e-7
MA0149.10.124
MA0150.10.773
MA0152.10.593
MA0153.18.24325e-48
MA0154.10.0244
MA0155.10.0561
MA0156.10.0789
MA0157.10.32
MA0159.10.00971
MA0160.10.132
MA0162.10.316
MA0163.10.0634
MA0164.10.895
MA0258.10.102
MA0259.10.0594



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: CNhs11098

Novel motifP-value
10.448
100.455
1000.389
1010.948
1020.571
1030.209
1040.676
1050.645
1060.0127
1070.00777
1080.754
1090.0802
110.409
1100.615
1110.273
1120.0257
1130.403
1140.488
1150.473
1160.212
1170.91
1180.725
1190.274
120.9
1200.997
1210.5
1220.662
1230.0804
1240.623
1250.832
1260.133
1270.903
1280.0603
1290.436
130.00109
1300.518
1310.0948
1320.165
1330.405
1340.337
1350.978
1360.0866
1370.766
1380.0265
1390.0663
140.567
1400.805
1410.319
1420.374
1430.106
1440.427
1450.212
1460.095
1470.855
1480.101
1490.0574
150.247
1500.27
1510.576
1520.0159
1530.429
1540.737
1550.719
1560.107
1570.556
1580.663
1590.134
1600.13
1610.244
1620.57
1630.0325
1640.233
1650.242
1660.933
1670.286
1680.242
1690.0193
170.126
180.757
190.0525
20.0562
200.342
210.833
220.209
230.314
240.712
250.921
260.00754
270.498
280.777
290.839
30.487
300.18
310.62
320.0179
330.263
340.351
350.913
360.477
370.0729
380.36
390.161
40.417
400.427
410.348
420.96
430.24
440.936
450.173
460.463
470.596
480.424
490.373
50.686
500.449
510.622
520.0284
530.607
540.595
550.417
560.383
570.346
580.541
590.094
60.638
600.034
610.391
620.868
630.287
640.878
650.25
660.382
670.251
680.564
690.89
70.126
700.291
710.224
720.714
730.149
740.804
750.425
760.286
770.0326
780.0553
790.817
80.733
800.742
810.52
820.171
830.91
840.565
850.12
860.337
870.19
880.996
890.151
90.536
900.697
910.854
920.399
930.99
940.113
950.241
960.5
970.378
980.805
990.0576



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: CNhs11098


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)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000305 (mouse neonate N10 sample)
0011418 (mouse intestine- neonate N10 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:0006595 (presumptive endoderm)
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:755-23A5&oldid=3267049"