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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008950
|DRA_sample_Accession=CAGE@SAMD00005884
|accession_numbers=CAGE;DRX009087;DRR009961;DRZ001386;DRZ002769
|accession_numbers=CAGE;DRX009087;DRR009961;DRZ001386;DRZ002769
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002106,UBERON:0002100,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002323,UBERON:0005177,UBERON:0004177,UBERON:0005057,UBERON:0005172,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0005173,UBERON:0002390,UBERON:0002417,UBERON:0002193,UBERON:0000916,UBERON:0002405
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002106,UBERON:0002100,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002323,UBERON:0005177,UBERON:0004177,UBERON:0005057,UBERON:0005172,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0005173,UBERON:0002390,UBERON:0002417,UBERON:0002193,UBERON:0000916,UBERON:0002405

Revision as of 22:01, 31 July 2014


Name:spleen, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11116
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuespleen
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  SAMD00005884
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11116 CAGE DRX009087 DRR009961
Accession ID Mm9

Library idBAMCTSS
CNhs11116 DRZ001386 DRZ002769
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

CNhs11116

00
10
100
1000
10000
10010.0119
10020.00471
1003-0.0927
10040
10050.075
1006-0.143
10070.0174
10080
1009-0.185
1010.103
10100
1011-0.103
10120.244
1013-0.0779
1014-0.0196
1015-0.164
1016-0.465
10170
10180
10190
1020
10200
10210.075
1022-0.165
10230
10240.049
10250
10260
10270
10280
10290.266
103-0.00877
10300.46
1031-0.188
1032-0.177
10330.00845
10340
10350
10360.411
10370
1038-0.255
1039-0.173
1040
1040-0.0915
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: CNhs11116

Jaspar motifP-value
MA0002.20.00953
MA0003.10.608
MA0004.10.937
MA0006.10.374
MA0007.10.785
MA0009.10.413
MA0014.10.991
MA0017.10.226
MA0018.29.60074e-4
MA0019.10.499
MA0024.15.21844e-7
MA0025.10.0555
MA0027.10.636
MA0028.10.0434
MA0029.10.964
MA0030.10.253
MA0031.10.502
MA0035.24.92642e-13
MA0038.10.0469
MA0039.20.718
MA0040.10.885
MA0041.10.3
MA0042.10.843
MA0043.15.52888e-4
MA0046.17.46664e-11
MA0047.20.834
MA0048.10.102
MA0050.11.27315e-5
MA0051.10.00112
MA0052.13.91262e-6
MA0055.10.188
MA0057.10.71
MA0058.10.964
MA0059.10.182
MA0060.10.267
MA0061.10.0101
MA0062.23.30613e-4
MA0065.20.29
MA0066.10.199
MA0067.10.574
MA0068.10.793
MA0069.10.497
MA0070.10.157
MA0071.10.724
MA0072.10.771
MA0073.10.868
MA0074.10.731
MA0076.10.0992
MA0077.10.0814
MA0078.10.508
MA0079.20.0329
MA0080.27.53797e-10
MA0081.10.0843
MA0083.10.143
MA0084.10.193
MA0087.10.0967
MA0088.10.108
MA0090.10.0563
MA0091.10.0211
MA0092.10.635
MA0093.10.989
MA0099.20.629
MA0100.10.0573
MA0101.10.0404
MA0102.20.917
MA0103.10.642
MA0104.20.638
MA0105.11.0843e-5
MA0106.10.314
MA0107.10.0738
MA0108.29.42747e-4
MA0111.10.668
MA0112.20.00124
MA0113.10.496
MA0114.10.722
MA0115.10.591
MA0116.14.71306e-4
MA0117.10.973
MA0119.10.107
MA0122.10.773
MA0124.10.88
MA0125.10.0657
MA0131.10.755
MA0135.10.076
MA0136.14.14394e-10
MA0137.20.754
MA0138.20.00512
MA0139.10.13
MA0140.11.01847e-45
MA0141.10.266
MA0142.10.36
MA0143.10.254
MA0144.10.785
MA0145.10.966
MA0146.10.474
MA0147.10.547
MA0148.10.657
MA0149.10.0235
MA0150.10.0303
MA0152.10.891
MA0153.11.30421e-6
MA0154.10.00593
MA0155.10.688
MA0156.16.46543e-8
MA0157.10.423
MA0159.10.272
MA0160.10.965
MA0162.10.186
MA0163.14.8273e-5
MA0164.10.456
MA0258.10.115
MA0259.10.857



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: CNhs11116

Novel motifP-value
10.0784
100.0244
1000.571
1010.97
1020.723
1030.0102
1040.865
1050.723
1060.243
1070.466
1080.362
1090.061
110.191
1100.0698
1110.0197
1120.0423
1130.995
1140.453
1150.528
1160.793
1170.00148
1180.112
1190.201
120.809
1200.873
1210.189
1220.59
1230.165
1240.881
1250.0208
1260.242
1270.444
1280.161
1290.197
130.00325
1300.277
1310.938
1320.168
1330.443
1340.0639
1350.928
1360.818
1370.0126
1380.626
1390.461
140.762
1400.202
1410.747
1420.0666
1430.453
1440.646
1450.00674
1460.851
1470.746
1480.123
1490.692
150.0463
1500.166
1510.326
1520.469
1530.593
1540.244
1550.0992
1560.771
1570.563
1580.0494
1590.0975
1600.434
1610.0804
1620.982
1630.716
1640.0224
1650.353
1660.381
1670.0746
1680.486
1690.0637
170.432
180.238
190.257
20.321
200.0745
210.421
220.638
230.892
240.435
250.361
268.08329e-4
270.85
280.287
290.016
30.0378
300.387
310.891
320.551
330.197
340.971
350.693
360.044
370.153
380.488
390.656
40.846
400.251
410.697
420.0532
430.0976
440.917
450.68
460.135
470.185
480.254
490.0583
50.0998
500.958
510.819
520.842
530.98
540.97
550.282
560.594
570.0651
580.315
590.494
60.382
600.394
610.438
620.15
630.41
640.576
650.539
660.782
670.429
680.689
690.279
70.0433
700.345
710.0173
720.409
730.445
740.712
750.0449
760.251
770.77
780.0426
790.989
80.0209
800.0596
810.437
820.599
830.485
840.0574
850.391
860.79
870.352
880.724
890.633
90.421
900.0241
910.127
920.461
930.451
940.119
950.193
960.00692
970.859
980.26
990.971



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: CNhs11116


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000305 (mouse neonate N10 sample)
0011417 (mouse spleen- 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:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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