Personal tools

FF:1517-43C4: 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=CNhs10598
|library_id=CNhs10598
|library_id_phase_based=1:CNhs10598
|name=forelimb, embryo E17
|name=forelimb, embryo E17
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 12:02, 18 June 2014


Name:forelimb, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs10598
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueforelimb
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  DRS008831
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10598 CAGE DRX008968 DRR009842
Accession ID Mm9

Library idBAMCTSS
CNhs10598 DRZ001267 DRZ002650
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

CNhs10598

00
10
100
1000
10000.0943
10010.0995
10020.0351
10030.417
10040
10050
1006-0.0559
10070.101
10080
10090.204
1010.0481
10100
10110.134
10120
1013-0.0754
10140.403
10150.0869
10160.224
10170.13
10180.49
10190
1020
10200
10210
10220
10230
10240.11
10250
10260
10270
10280
10290.28
1030.694
10300
10310.365
10320.0199
10330.0484
10340
10350
10360.159
10370
10380.00596
1039-0.119
1040
10400.229
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: CNhs10598

Jaspar motifP-value
MA0002.20.133
MA0003.10.342
MA0004.10.297
MA0006.10.237
MA0007.10.547
MA0009.10.896
MA0014.10.202
MA0017.11.04364e-13
MA0018.20.0106
MA0019.10.245
MA0024.10.36
MA0025.10.17
MA0027.10.0979
MA0028.12.67237e-5
MA0029.10.824
MA0030.10.27
MA0031.10.0899
MA0035.25.59515e-5
MA0038.10.141
MA0039.20.101
MA0040.10.074
MA0041.10.0527
MA0042.10.233
MA0043.10.797
MA0046.11.14943e-17
MA0047.20.0057
MA0048.10.253
MA0050.11.95109e-5
MA0051.18.54274e-5
MA0052.12.69838e-14
MA0055.10.0149
MA0057.10.662
MA0058.10.138
MA0059.10.0189
MA0060.10.206
MA0061.10.552
MA0062.29.18134e-9
MA0065.23.11823e-4
MA0066.10.504
MA0067.10.202
MA0068.10.271
MA0069.10.707
MA0070.10.983
MA0071.13.59908e-4
MA0072.10.0221
MA0073.10.649
MA0074.10.235
MA0076.13.82286e-5
MA0077.10.946
MA0078.10.231
MA0079.20.0264
MA0080.22.22637e-6
MA0081.10.0714
MA0083.10.0175
MA0084.10.656
MA0087.10.561
MA0088.10.838
MA0090.10.0649
MA0091.10.689
MA0092.10.66
MA0093.10.334
MA0099.20.00355
MA0100.10.0809
MA0101.10.313
MA0102.20.739
MA0103.10.0594
MA0104.20.0743
MA0105.10.637
MA0106.10.335
MA0107.10.437
MA0108.23.45931e-23
MA0111.10.296
MA0112.20.181
MA0113.10.0616
MA0114.13.03472e-11
MA0115.12.62546e-5
MA0116.10.116
MA0117.10.184
MA0119.10.411
MA0122.10.761
MA0124.10.198
MA0125.10.00673
MA0131.10.849
MA0135.10.209
MA0136.19.2969e-8
MA0137.20.125
MA0138.20.137
MA0139.10.0155
MA0140.18.69891e-4
MA0141.12.16858e-9
MA0142.10.15
MA0143.10.4
MA0144.10.295
MA0145.10.0608
MA0146.10.75
MA0147.10.0403
MA0148.10.00228
MA0149.10.0029
MA0150.10.00819
MA0152.10.0169
MA0153.13.33566e-12
MA0154.10.385
MA0155.10.62
MA0156.15.59956e-6
MA0157.10.922
MA0159.17.31249e-4
MA0160.15.00689e-6
MA0162.10.963
MA0163.10.18
MA0164.10.722
MA0258.10.0131
MA0259.10.404



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: CNhs10598

Novel motifP-value
10.164
100.226
1000.987
1010.567
1020.652
1030.0875
1040.285
1050.869
1060.99
1070.319
1080.874
1090.379
110.0714
1100.461
1110.0607
1120.0584
1130.873
1140.0867
1150.649
1160.713
1170.0696
1180.0741
1190.192
120.524
1200.448
1210.309
1220.469
1230.478
1240.494
1250.082
1260.43
1270.754
1280.716
1290.411
130.821
1300.426
1310.594
1320.732
1330.438
1340.306
1350.629
1360.564
1370.919
1380.782
1390.155
140.976
1400.626
1410.585
1420.636
1430.178
1440.141
1450.268
1460.987
1470.198
1480.383
1490.719
150.00867
1500.852
1510.149
1520.0414
1530.721
1540.575
1550.543
1561.48154e-5
1570.255
1580.328
1591
1600.203
1610.407
1620.964
1630.426
1640.0977
1650.179
1660.118
1670.0904
1680.162
1690.0715
170.974
180.15
190.726
20.184
200.14
210.966
220.465
230.489
240.957
250.286
260.236
270.389
280.483
290.042
30.182
300.0807
310.323
320.625
330.285
340.46
350.00555
360.0153
370.737
380.453
390.804
40.893
400.0471
410.508
420.7
430.313
440.0797
450.192
460.84
470.304
480.128
490.0471
50.374
500.284
510.754
520.329
530.553
540.847
550.529
560.803
570.553
580.753
590.7
60.781
600.647
610.78
620.351
630.916
640.19
650.339
660.991
670.682
680.00461
690.988
70.956
700.146
710.543
720.459
730.819
740.7
750.134
760.0234
770.79
780.5
790.425
80.04
800.0485
810.724
820.447
830.384
840.82
850.497
860.529
870.113
880.934
890.7
90.582
900.0345
910.801
920.553
930.294
940.384
950.245
960.858
970.992
980.272
990.673



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: CNhs10598


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)
0002102 (forelimb)
0000479 (tissue)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
0004708 (paired limb/fin)
0002101 (limb)
0004710 (pectoral appendage)
0010317 (germ layer / neural crest derived structure)
0010707 (appendage girdle complex)
0000153 (anterior region of body)
0010708 (pectoral complex)

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)
0011277 (mouse forelimb- 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:0006603 (presumptive mesoderm)
UBERON:0005417 (forelimb bud)
UBERON:0005733 (limb field)
UBERON:0005732 (limb/fin field)
UBERON:0005729 (forelimb/pectoral fin field)
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:1517-43C4&oldid=3267017"