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|sample_age=
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|sample_category=developmental
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|sample_cell_line=
|sample_cell_line=

Revision as of 15:42, 26 December 2012


Name:spleen, adult
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuespleen
dev stageadult
sexmale
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
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

CNhs10465

00
10
100
1000
10000
10010
10020.0171
1003-0.0527
10040
10050.128
1006-0.143
1007-0.025
10080
1009-0.0624
1010.0816
10100
10110.0202
10120.128
1013-0.0433
1014-0.0874
1015-0.234
1016-0.466
10170
10180
10190
1020
10200
10210.079
1022-0.185
10230
1024-0.0504
1025-0.0295
10260
10270
10280
10290.0321
103-0.0736
10300.374
1031-0.348
1032-0.281
10330.0612
10340
10350
10360.13
10370
1038-0.304
1039-0.221
1040
1040-0.121
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: CNhs10465

Jaspar motifP-value
MA0002.22.03443e-7
MA0003.10.844
MA0004.10.733
MA0006.10.253
MA0007.10.664
MA0009.10.653
MA0014.10.692
MA0017.10.313
MA0018.20.007
MA0019.10.184
MA0024.10.0145
MA0025.10.562
MA0027.10.505
MA0028.10.0518
MA0029.10.824
MA0030.10.306
MA0031.10.921
MA0035.24.55585e-6
MA0038.10.0689
MA0039.20.345
MA0040.10.248
MA0041.10.377
MA0042.10.936
MA0043.10.0129
MA0046.13.06436e-12
MA0047.20.497
MA0048.10.596
MA0050.11.84537e-14
MA0051.11.09493e-8
MA0052.13.98578e-5
MA0055.10.599
MA0057.10.729
MA0058.10.838
MA0059.10.471
MA0060.10.893
MA0061.14.59346e-5
MA0062.22.70737e-7
MA0065.20.36
MA0066.10.177
MA0067.10.787
MA0068.10.696
MA0069.10.436
MA0070.10.535
MA0071.10.839
MA0072.10.464
MA0073.10.889
MA0074.10.615
MA0076.10.0971
MA0077.10.197
MA0078.10.838
MA0079.20.0685
MA0080.23.45622e-14
MA0081.10.00717
MA0083.10.154
MA0084.10.287
MA0087.10.0877
MA0088.10.254
MA0090.10.0267
MA0091.10.221
MA0092.10.696
MA0093.10.831
MA0099.20.953
MA0100.10.18
MA0101.13.81156e-4
MA0102.20.317
MA0103.10.722
MA0104.20.826
MA0105.15.29559e-7
MA0106.10.622
MA0107.11.7784e-4
MA0108.20.00332
MA0111.10.743
MA0112.20.00118
MA0113.10.24
MA0114.10.936
MA0115.10.992
MA0116.10.00202
MA0117.10.688
MA0119.10.41
MA0122.10.946
MA0124.10.79
MA0125.10.046
MA0131.10.876
MA0135.10.288
MA0136.16.47913e-20
MA0137.20.155
MA0138.20.0118
MA0139.10.224
MA0140.12.2068e-27
MA0141.10.778
MA0142.16.0363e-5
MA0143.10.136
MA0144.10.322
MA0145.10.618
MA0146.10.186
MA0147.10.763
MA0148.10.66
MA0149.10.154
MA0150.10.0118
MA0152.10.403
MA0153.15.19293e-8
MA0154.10.0011
MA0155.10.681
MA0156.11.00735e-16
MA0157.10.993
MA0159.10.0859
MA0160.10.981
MA0162.10.142
MA0163.13.24261e-4
MA0164.10.42
MA0258.10.0622
MA0259.10.68



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: CNhs10465

Novel motifP-value
10.176
100.0389
1000.922
1010.84
1020.61
1030.037
1040.99
1050.899
1060.0977
1070.552
1080.593
1090.0864
110.119
1100.0773
1110.0768
1120.0241
1130.427
1140.313
1150.889
1160.776
1170.00171
1180.104
1190.116
120.806
1200.789
1210.144
1220.848
1230.316
1240.841
1250.0538
1260.215
1270.372
1280.139
1290.221
130.0453
1300.34
1310.911
1320.189
1330.941
1340.3
1350.93
1360.513
1370.044
1380.919
1390.538
140.637
1400.693
1410.288
1420.28
1430.0872
1440.792
1450.0353
1460.739
1470.688
1480.0746
1490.661
150.0223
1500.135
1510.125
1520.812
1530.433
1540.799
1550.132
1560.0692
1570.843
1580.0519
1590.396
1600.542
1610.0445
1620.431
1630.441
1640.0544
1650.163
1660.396
1670.446
1680.448
1690.0199
170.336
180.128
190.306
20.495
200.142
210.27
220.382
230.605
240.168
250.269
260.00456
270.419
280.167
290.0409
30.038
300.471
310.661
320.609
330.198
340.66
350.456
360.105
370.159
380.241
390.743
40.998
400.212
410.838
420.0603
430.0614
440.264
450.882
460.132
470.126
480.19
490.0878
50.111
500.871
510.829
520.757
530.857
540.999
550.144
560.429
570.416
580.199
590.155
60.511
600.256
610.233
620.0687
630.314
640.487
650.201
660.722
670.522
680.174
690.746
70.0712
700.175
710.034
720.256
730.179
740.687
750.0269
760.226
770.747
780.027
790.764
80.0293
800.00288
810.398
820.457
830.127
840.515
850.152
860.414
870.387
880.577
890.744
90.424
900.0852
910.28
920.456
930.164
940.101
950.116
960.108
970.871
980.108
990.693



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: CNhs10465


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)
0007023 (adult 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)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011306 (mouse spleen- adult 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)

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