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|name=spleen, embryo E16
 
|name=spleen, embryo E16
 
|namespace=FANTOM5
 
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Revision as of 03:17, 18 June 2014


Name:spleen, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs11035
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuespleen
dev stage16 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  DRS008948
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11035 CAGE DRX009085 DRR009959
Accession ID Mm9

Library idBAMCTSS
CNhs11035 DRZ001384 DRZ002767
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

CNhs11035

00
10
100
1000
10000.00363
1001-0.0631
10020.239
10030.0389
10040
10050.109
1006-0.107
10070.0301
10080
10090.152
1010.049
10100.209
1011-0.00851
10120
1013-0.0113
10140.209
10150.135
10160.187
10170.0815
10180.0815
10190
1020
10200
10210
1022-0.142
10230
1024-0.00131
10250.247
10260
10270
10280
1029-0.0945
1030.259
10300
10310.329
1032-0.0782
10330.015
10340.0301
10350
10360.123
10370
10380.0487
1039-0.125
1040
10400.202
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: CNhs11035

Jaspar motifP-value
MA0002.20.111
MA0003.10.174
MA0004.10.57
MA0006.10.0942
MA0007.10.892
MA0009.10.251
MA0014.10.811
MA0017.10.00213
MA0018.21.75304e-7
MA0019.10.165
MA0024.18.53203e-13
MA0025.10.00175
MA0027.10.00875
MA0028.10.499
MA0029.10.841
MA0030.10.222
MA0031.10.0174
MA0035.20.0104
MA0038.10.506
MA0039.20.0291
MA0040.10.442
MA0041.10.413
MA0042.10.48
MA0043.10.0115
MA0046.10.00524
MA0047.20.456
MA0048.10.0187
MA0050.10.115
MA0051.10.3
MA0052.11.33787e-5
MA0055.10.0236
MA0057.10.91
MA0058.10.587
MA0059.10.567
MA0060.17.32359e-4
MA0061.10.0174
MA0062.20.0236
MA0065.20.00318
MA0066.10.451
MA0067.10.0303
MA0068.10.241
MA0069.10.834
MA0070.10.819
MA0071.10.0489
MA0072.10.249
MA0073.10.997
MA0074.10.0838
MA0076.10.395
MA0077.10.64
MA0078.10.501
MA0079.20.031
MA0080.23.55221e-12
MA0081.10.00231
MA0083.10.26
MA0084.10.554
MA0087.10.178
MA0088.10.762
MA0090.10.575
MA0091.10.481
MA0092.10.56
MA0093.10.72
MA0099.20.00318
MA0100.10.469
MA0101.10.0825
MA0102.20.222
MA0103.12.75319e-5
MA0104.20.123
MA0105.10.0227
MA0106.10.123
MA0107.10.0837
MA0108.20.84
MA0111.10.939
MA0112.20.985
MA0113.10.25
MA0114.12.24783e-5
MA0115.12.99192e-4
MA0116.10.399
MA0117.10.0048
MA0119.10.241
MA0122.10.468
MA0124.10.328
MA0125.10.532
MA0131.10.884
MA0135.10.651
MA0136.16.67065e-12
MA0137.20.667
MA0138.20.00828
MA0139.10.14
MA0140.15.72709e-8
MA0141.10.00178
MA0142.10.876
MA0143.10.585
MA0144.10.81
MA0145.10.735
MA0146.10.234
MA0147.10.242
MA0148.10.611
MA0149.10.28
MA0150.10.0446
MA0152.10.572
MA0153.15.99419e-4
MA0154.10.00626
MA0155.10.0504
MA0156.11.14231e-12
MA0157.10.252
MA0159.10.0433
MA0160.10.0154
MA0162.10.321
MA0163.10.0108
MA0164.10.368
MA0258.10.216
MA0259.10.753



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: CNhs11035

Novel motifP-value
10.191
100.966
1000.645
1010.622
1020.765
1030.881
1040.886
1050.54
1060.48
1070.281
1080.958
1090.0826
110.751
1100.69
1110.206
1120.461
1130.971
1140.078
1150.322
1160.242
1170.854
1180.967
1190.382
120.223
1200.432
1210.918
1220.864
1230.0173
1240.5
1250.348
1260.582
1270.613
1280.717
1290.209
130.027
1300.00615
1310.909
1320.399
1330.103
1340.187
1350.319
1360.0614
1370.07
1380.00642
1390.0737
140.863
1400.576
1410.987
1420.814
1430.476
1440.526
1450.0526
1460.822
1470.289
1480.122
1490.434
150.731
1500.0513
1510.608
1520.117
1530.525
1540.393
1550.437
1562.75692e-5
1570.818
1580.99
1590.308
1600.0431
1610.0324
1620.622
1630.76
1640.581
1650.228
1660.344
1670.413
1680.855
1690.139
170.391
180.28
190.112
20.79
200.994
210.0841
220.242
230.259
240.00212
250.11
260.0188
270.962
280.231
290.928
30.916
300.638
310.545
320.307
330.177
340.381
350.0293
360.711
370.455
380.765
390.638
40.558
400.695
410.387
420.275
430.935
440.0657
450.722
460.692
470.406
480.608
490.295
50.507
500.0571
510.55
520.494
530.601
540.377
550.581
560.716
570.657
580.581
590.177
60.623
600.5
610.146
620.192
630.777
640.793
650.956
660.991
670.874
680.0547
690.944
70.543
700.00333
710.421
720.139
730.124
740.571
750.852
760.72
770.825
780.301
790.617
80.795
800.542
810.654
820.559
830.436
840.00312
850.233
860.921
870.617
880.767
890.499
90.244
900.257
910.761
920.441
930.91
940.717
950.12
960.35
970.909
980.477
990.186



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: CNhs11035


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)
0002106 (spleen)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002323 (body cavity)
0005177 (trunk region element)
0004177 (hemopoietic organ)
0005057 (immune organ)
0005172 (abdomen element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002390 (hematopoietic system)
0002417 (abdominal segment of trunk)
0002193 (hemolymphoid system)
0000916 (abdomen)
0002405 (immune 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)
0000299 (mouse embryonic day 16 sample)
0011360 (mouse spleen- embryo E16 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:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)