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{{f5samples
 
{{f5samples
|DRA_sample_Accession=CAGE@DRS008847
+
|DRA_sample_Accession=CAGE@SAMD00005134
 
|accession_numbers=CAGE;DRX008984;DRR009858;DRZ001283;DRZ002666
 
|accession_numbers=CAGE;DRX008984;DRR009858;DRZ001283;DRZ002666
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007100,UBERON:0000948,UBERON:0000479,UBERON:0010314,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0010317,UBERON:0004535,UBERON:0001009
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007100,UBERON:0000948,UBERON:0000479,UBERON:0010314,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0010317,UBERON:0004535,UBERON:0001009

Revision as of 12:36, 31 July 2014


Name:heart, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11196
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueheart
dev stage25 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  SAMD00005134
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11196 CAGE DRX008984 DRR009858
Accession ID Mm9

Library idBAMCTSS
CNhs11196 DRZ001283 DRZ002666
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

CNhs11196

00
10
100.854
1000
10000.812
10010.701
10020.0754
10030.18
10040
10050
10060.575
1007-0.151
10080
10090.25
101-0.0446
10100
10110
10120.0862
1013-0.0775
1014-0.00116
1015-0.256
10160.0121
10170
10180
10190
1020
10200
10210
10220.717
10230
10240.458
10250
10260.0862
10270.0252
10280
10290.0978
1030.0637
10300
1031-0.0306
10320.132
10330
10340
10350.404
1036-0.307
10370
10380.0914
10390.641
1040
10400.219
10410.322



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: CNhs11196

Jaspar motifP-value
MA0002.20.731
MA0003.10.277
MA0004.10.0746
MA0006.10.205
MA0007.10.985
MA0009.10.862
MA0014.10.634
MA0017.10.68
MA0018.20.0981
MA0019.10.167
MA0024.14.37417e-4
MA0025.10.486
MA0027.10.398
MA0028.10.0257
MA0029.10.802
MA0030.10.162
MA0031.10.457
MA0035.23.31506e-5
MA0038.10.613
MA0039.20.676
MA0040.10.254
MA0041.10.387
MA0042.10.435
MA0043.10.133
MA0046.11.50793e-15
MA0047.20.68
MA0048.10.722
MA0050.10.0355
MA0051.10.0257
MA0052.11.50826e-51
MA0055.10.464
MA0057.10.591
MA0058.10.0445
MA0059.10.159
MA0060.12.58092e-11
MA0061.10.517
MA0062.24.46631e-5
MA0065.20.00727
MA0066.10.834
MA0067.10.403
MA0068.10.855
MA0069.10.184
MA0070.10.943
MA0071.10.00983
MA0072.10.657
MA0073.10.859
MA0074.10.201
MA0076.10.00193
MA0077.10.835
MA0078.10.701
MA0079.20.77
MA0080.20.237
MA0081.10.848
MA0083.17.71115e-11
MA0084.10.5
MA0087.10.529
MA0088.10.707
MA0090.11.45143e-4
MA0091.10.492
MA0092.10.412
MA0093.10.058
MA0099.20.333
MA0100.10.0182
MA0101.10.938
MA0102.20.225
MA0103.10.00541
MA0104.20.0534
MA0105.10.376
MA0106.10.351
MA0107.10.576
MA0108.20.377
MA0111.10.783
MA0112.21.44568e-6
MA0113.10.334
MA0114.10.934
MA0115.10.185
MA0116.10.755
MA0117.10.547
MA0119.10.124
MA0122.10.0331
MA0124.10.759
MA0125.10.247
MA0131.10.167
MA0135.10.141
MA0136.10.00454
MA0137.20.265
MA0138.20.00631
MA0139.10.688
MA0140.10.00186
MA0141.13.73787e-9
MA0142.10.363
MA0143.10.172
MA0144.10.508
MA0145.10.0498
MA0146.10.0631
MA0147.10.115
MA0148.10.761
MA0149.10.863
MA0150.10.0537
MA0152.10.215
MA0153.15.20794e-10
MA0154.10.0134
MA0155.10.283
MA0156.10.0429
MA0157.10.89
MA0159.19.35272e-6
MA0160.11.86427e-5
MA0162.10.0834
MA0163.10.11
MA0164.10.298
MA0258.10.00165
MA0259.10.205



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: CNhs11196

Novel motifP-value
10.0775
100.583
1000.675
1010.714
1020.772
1030.374
1040.65
1050.101
1060.193
1070.153
1080.673
1090.154
110.278
1100.154
1110.0173
1120.597
1130.666
1140.0793
1150.55
1160.967
1170.785
1180.784
1190.08
120.918
1200.205
1210.164
1220.654
1230.517
1240.689
1250.697
1260.635
1270.469
1280.444
1290.0495
130.00142
1300.791
1310.868
1320.767
1330.575
1340.609
1350.812
1360.48
1370.551
1380.115
1390.078
140.149
1400.311
1410.439
1420.917
1430.461
1440.453
1450.409
1460.631
1470.501
1480.345
1490.00312
150.251
1500.412
1510.149
1520.0717
1530.462
1540.949
1550.0551
1560.178
1570.874
1580.0941
1590.0364
1600.248
1610.942
1620.538
1630.274
1640.382
1653.4078e-4
1660.214
1670.905
1680.0798
1697.75013e-5
170.11
180.376
190.0348
20.592
200.746
210.326
220.028
230.323
240.833
250.721
260.0912
270.903
280.813
290.896
30.259
300.57
310.394
320.926
330.73
340.2
350.965
360.66
370.0145
380.623
390.623
40.413
400.902
410.559
420.758
430.151
440.75
450.531
460.483
470.437
480.423
490.155
50.187
500.604
510.501
520.313
530.692
540.39
550.921
560.406
570.377
580.383
590.0266
60.179
600.181
610.602
620.342
630.0769
640.667
650.432
660.137
670.709
680.857
690.124
70.0995
700.304
710.0659
720.904
730.0466
740.256
750.543
760.862
770.224
780.0321
790.912
80.425
800.509
810.387
820.0874
830.283
840.21
850.00379
860.704
870.0543
880.534
890.0445
90.129
900.442
910.331
920.129
930.77
940.499
950.246
960.481
970.372
980.245
990.736



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: CNhs11196


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000309 (mouse neonate N25 sample)
0011475 (mouse heart- neonate N25 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)