Personal tools

FF:403-26D4

From FANTOM5_SSTAR

Revision as of 11:05, 28 November 2014 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:heart, embryo E14
Species:Mouse (Mus musculus)
Library ID:CNhs10597
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueheart
dev stage14 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  SAMD00004723
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10597 CAGE DRX008974 DRR009848
Accession ID Mm9

Library idBAMCTSS
CNhs10597 DRZ001273 DRZ002656
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

CNhs10597

00
10
100.168
1000
10000.224
10010.229
10020.42
10030.031
10040
1005-0.0389
10060.13
10070.0374
10080
10090.176
1010.0272
10100
10110.00205
10120
1013-0.206
10140.337
10150.0796
10160.182
10170
10180
10190
1020
10200
10210
10220.372
10230
10240.168
10250.168
10260
10270
10280
10290.162
1030.121
10300
10310.433
10320.0165
1033-0.0665
10340
10350.339
1036-0.107
10370
10380.0733
10390.0767
1040
10400.173
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: CNhs10597

Jaspar motifP-value
MA0002.20.0105
MA0003.10.766
MA0004.10.552
MA0006.10.779
MA0007.10.138
MA0009.10.862
MA0014.10.909
MA0017.16.43601e-5
MA0018.20.824
MA0019.10.869
MA0024.19.77362e-5
MA0025.10.628
MA0027.10.0642
MA0028.10.227
MA0029.10.583
MA0030.10.283
MA0031.10.195
MA0035.20.139
MA0038.10.559
MA0039.20.0577
MA0040.10.112
MA0041.10.809
MA0042.10.659
MA0043.10.998
MA0046.11.65958e-17
MA0047.20.0973
MA0048.10.286
MA0050.12.12038e-6
MA0051.10.00843
MA0052.16.37523e-32
MA0055.10.0176
MA0057.10.745
MA0058.10.716
MA0059.10.437
MA0060.10.038
MA0061.10.038
MA0062.25.7074e-4
MA0065.20.0133
MA0066.10.321
MA0067.10.896
MA0068.10.214
MA0069.10.548
MA0070.10.784
MA0071.10.358
MA0072.10.0649
MA0073.10.952
MA0074.10.845
MA0076.10.078
MA0077.10.345
MA0078.10.228
MA0079.20.259
MA0080.20.0259
MA0081.10.95
MA0083.11.59054e-17
MA0084.10.726
MA0087.10.574
MA0088.10.0746
MA0090.10.00177
MA0091.10.439
MA0092.10.991
MA0093.10.631
MA0099.26.86176e-6
MA0100.10.924
MA0101.10.118
MA0102.20.00825
MA0103.11.80007e-6
MA0104.20.645
MA0105.10.0758
MA0106.10.406
MA0107.10.187
MA0108.20.135
MA0111.10.293
MA0112.20.35
MA0113.10.964
MA0114.12.8122e-7
MA0115.10.37
MA0116.10.00114
MA0117.10.159
MA0119.10.373
MA0122.10.397
MA0124.10.264
MA0125.10.442
MA0131.10.703
MA0135.10.93
MA0136.10.0192
MA0137.20.00876
MA0138.20.072
MA0139.10.0477
MA0140.10.2
MA0141.10.161
MA0142.10.517
MA0143.10.778
MA0144.10.219
MA0145.10.237
MA0146.10.917
MA0147.10.414
MA0148.10.076
MA0149.10.0721
MA0150.11.62098e-4
MA0152.10.732
MA0153.11.6555e-11
MA0154.10.104
MA0155.10.152
MA0156.10.00276
MA0157.10.268
MA0159.10.917
MA0160.10.42
MA0162.10.452
MA0163.10.354
MA0164.10.396
MA0258.10.143
MA0259.10.807



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: CNhs10597

Novel motifP-value
10.3
100.153
1000.601
1010.959
1020.552
1030.025
1040.796
1050.726
1060.411
1070.965
1080.774
1090.388
110.0988
1100.791
1110.96
1120.105
1130.922
1140.266
1150.673
1160.149
1170.507
1180.99
1190.152
120.44
1200.252
1210.937
1220.4
1230.124
1240.993
1250.719
1260.569
1270.218
1280.0505
1290.255
130.105
1300.175
1310.632
1320.956
1330.895
1340.702
1350.781
1360.152
1370.703
1380.104
1390.499
140.784
1400.763
1410.0645
1420.646
1430.391
1440.239
1450.508
1460.601
1470.714
1480.527
1490.928
150.132
1500.515
1510.0713
1520.804
1530.133
1540.737
1550.104
1560.219
1570.712
1580.639
1590.189
1600.399
1610.707
1620.925
1630.748
1640.278
1650.928
1660.506
1670.387
1680.968
1690.222
170.0467
180.086
190.826
20.722
200.826
210.785
220.629
230.191
240.918
250.32
260.187
270.387
280.239
290.833
30.0868
300.203
310.34
320.393
330.0947
340.496
350.0447
360.076
370.523
380.395
390.488
40.56
400.00697
410.976
420.191
430.176
440.545
450.421
460.494
470.394
480.271
490.236
50.438
500.559
510.793
520.815
530.898
540.578
550.262
560.52
570.745
580.481
590.362
60.0467
600.444
610.844
620.187
630.741
640.463
650.228
660.896
670.926
680.238
690.426
70.947
700.00146
710.928
720.128
730.541
740.763
750.02
760.798
770.221
780.621
790.124
80.139
800.0495
810.418
820.187
830.563
840.442
850.483
860.636
870.00125
880.36
890.25
90.682
900.113
910.664
920.132
930.279
940.888
950.439
960.569
970.198
980.187
990.51



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: CNhs10597


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)
0007100 (primary circulatory organ)
0000948 (heart)
0000479 (tissue)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0010317 (germ layer / neural crest derived structure)
0004535 (cardiovascular system)
0001009 (circulatory 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)
0000296 (mouse embryonic day 14 sample)
0011337 (mouse heart- embryo E14 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:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0004140 (primary heart 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:403-26D4&oldid=3284003"