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|library_id_phase_based=1:CNhs11104
|name=stomach, neonate N25
|name=stomach, neonate N25
|namespace=FANTOM5
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Revision as of 12:18, 18 June 2014


Name:stomach, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11104
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuestomach
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  DRS008961
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11104 CAGE DRX009098 DRR009972
Accession ID Mm9

Library idBAMCTSS
CNhs11104 DRZ001397 DRZ002780
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

CNhs11104

00
10
100
1000
10000.3
10010.0966
10020.322
10030.0426
10040
10050.0328
10060.0351
1007-0.0222
10080
10090.243
101-0.0783
10100
1011-0.0339
10120
10130.33
10140
1015-0.237
1016-0.154
10170.252
10180.617
10190
1020
10200
10210
10220.363
10230
10240.145
10250.72
10260
10277.687337e-4
10280
10290.135
1030.216
10300
10310.0211
10320.271
1033-0.0665
10340.41
10350
1036-0.0983
10370
10380.121
10390.388
1040
10400.0928
10410.101



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: CNhs11104

Jaspar motifP-value
MA0002.20.356
MA0003.10.226
MA0004.10.481
MA0006.10.0616
MA0007.10.149
MA0009.10.0279
MA0014.10.362
MA0017.10.755
MA0018.20.00343
MA0019.10.556
MA0024.19.45939e-5
MA0025.10.301
MA0027.10.41
MA0028.10.0392
MA0029.10.856
MA0030.10.0345
MA0031.10.0124
MA0035.20.251
MA0038.10.671
MA0039.23.39725e-4
MA0040.10.512
MA0041.10.374
MA0042.10.255
MA0043.12.49607e-4
MA0046.12.00532e-9
MA0047.26.16337e-11
MA0048.10.442
MA0050.10.116
MA0051.10.457
MA0052.10.032
MA0055.10.148
MA0057.10.0398
MA0058.10.251
MA0059.10.505
MA0060.10.00125
MA0061.10.997
MA0062.20.00127
MA0065.20.0902
MA0066.10.314
MA0067.10.921
MA0068.10.0814
MA0069.10.106
MA0070.10.834
MA0071.10.304
MA0072.10.791
MA0073.10.961
MA0074.10.528
MA0076.10.0121
MA0077.10.161
MA0078.10.0644
MA0079.20.0541
MA0080.20.766
MA0081.10.0475
MA0083.13.28332e-7
MA0084.10.998
MA0087.10.514
MA0088.10.713
MA0090.16.15806e-4
MA0091.10.926
MA0092.10.174
MA0093.10.405
MA0099.27.34574e-13
MA0100.10.0225
MA0101.10.563
MA0102.20.337
MA0103.11.83476e-5
MA0104.20.101
MA0105.10.908
MA0106.10.0243
MA0107.10.65
MA0108.21.72586e-8
MA0111.10.492
MA0112.22.9478e-4
MA0113.10.468
MA0114.10.733
MA0115.10.0937
MA0116.10.526
MA0117.10.873
MA0119.10.147
MA0122.10.964
MA0124.10.663
MA0125.10.0955
MA0131.10.185
MA0135.10.324
MA0136.10.0978
MA0137.20.933
MA0138.20.0278
MA0139.10.172
MA0140.10.797
MA0141.10.524
MA0142.10.107
MA0143.10.0339
MA0144.10.463
MA0145.10.00116
MA0146.10.169
MA0147.10.0975
MA0148.11.51974e-11
MA0149.10.371
MA0150.10.256
MA0152.10.299
MA0153.11.30667e-7
MA0154.10.0413
MA0155.10.868
MA0156.10.232
MA0157.10.0257
MA0159.10.104
MA0160.10.966
MA0162.10.404
MA0163.10.72
MA0164.10.57
MA0258.10.0178
MA0259.10.0948



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: CNhs11104

Novel motifP-value
10.337
100.903
1000.548
1010.847
1020.367
1030.177
1040.6
1050.26
1060.00239
1070.0205
1080.785
1090.123
110.579
1100.528
1110.267
1120.328
1130.815
1140.999
1150.797
1160.37
1170.716
1180.272
1190.0123
120.967
1200.951
1210.741
1220.556
1230.493
1240.739
1250.781
1260.109
1270.715
1280.011
1290.868
130.0192
1300.978
1310.731
1320.775
1330.52
1340.724
1350.399
1360.503
1370.45
1380.294
1390.0892
140.44
1400.0781
1410.264
1420.979
1430.0609
1440.261
1450.18
1460.101
1470.805
1480.764
1490.0199
150.328
1500.351
1510.407
1520.00796
1530.774
1540.856
1550.889
1560.00331
1570.135
1580.772
1590.934
1600.32
1610.486
1620.335
1630.939
1640.887
1650.394
1660.137
1670.37
1680.0662
1690.0049
170.028
180.49
190.1
20.175
200.286
210.847
220.243
230.187
240.119
250.835
260.0779
270.574
280.673
290.909
30.598
300.167
310.492
320.0159
330.804
340.537
350.623
360.548
370.0443
380.61
390.258
40.00481
400.587
410.318
420.859
430.258
440.592
450.206
460.316
470.471
480.606
490.309
50.527
500.578
510.543
520.0348
530.428
540.276
550.242
560.356
570.663
580.465
590.201
60.312
600.03
610.365
620.4
630.125
640.981
650.329
660.927
670.689
680.584
690.943
70.176
700.0455
710.22
720.73
730.0306
740.838
750.639
760.111
770.0164
780.112
790.635
80.474
800.506
810.373
820.159
830.931
840.517
850.0246
860.36
870.222
880.446
890.137
90.345
900.872
910.891
920.146
930.9
940.405
950.183
960.066
970.0198
980.674
990.0618



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: CNhs11104


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)
0000945 (stomach)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010039 (food storage organ)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001041 (foregut)

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)
0011493 (mouse stomach- 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:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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