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{{f5samples
{{f5samples
|id=FF:1548-44H5
|id=FF:1548-44H5
|name=pancreas, neonate N30, biol_rep1
|name=pancreas, neonate N30
|sample_id=1548
|sample_id=1548
|rna_tube_id=1548-44H5
|rna_tube_id=44H5
|rna_box=1548-44H5
|rna_box=44
|rna_position=1548-44H5
|rna_position=H5
|sample_cell_lot=
|sample_cell_lot=
|sample_cell_catalog=
|sample_cell_catalog=
Line 32: Line 32:
|rna_concentration=
|rna_concentration=
|sample_note=
|sample_note=
|profile_hcage=CNhs11182,LSID746,,COMPLETED
|profile_hcage=CNhs11182,LSID746,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:50, 27 February 2012


Name:pancreas, neonate N30
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepancreas
dev stage30 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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs11182

00
10
100
1000
10000
1001-0.0233
1002-0.0941
1003-0.123
10040
10050
1006-0.0539
10070.128
10080
10090.0481
101-0.0247
10100
1011-0.269
10120
10130.628
1014-0.0874
1015-0.294
1016-0.286
10170
10180.0162
10190
1020
10200
10210.243
10220.736
10230
10240
1025-0.0611
10260
1027-0.048
10280
1029-0.148
103-0.0317
10300
1031-0.178
10320.134
10330
10341.235
10350
1036-0.183
10370
10380.202
10390.267
1040
1040-0.11
10410.308



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 no result for this sample


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: CNhs11182

Jaspar motifP-value
MA0002.20.307
MA0003.10.587
MA0004.10.269
MA0006.10.142
MA0007.10.408
MA0009.10.711
MA0014.10.273
MA0017.10.232
MA0018.20.00566
MA0019.10.754
MA0024.10.00292
MA0025.10.158
MA0027.10.81
MA0028.10.807
MA0029.10.889
MA0030.10.942
MA0031.10.51
MA0035.20.0919
MA0038.10.343
MA0039.20.0415
MA0040.10.753
MA0041.10.173
MA0042.10.532
MA0043.10.0645
MA0046.11.31132e-8
MA0047.22.22179e-4
MA0048.10.838
MA0050.10.564
MA0051.10.409
MA0052.10.00129
MA0055.10.435
MA0057.10.135
MA0058.10.318
MA0059.10.0105
MA0060.17.5109e-4
MA0061.10.815
MA0062.20.902
MA0065.20.0396
MA0066.10.47
MA0067.10.0688
MA0068.10.165
MA0069.10.552
MA0070.10.807
MA0071.10.204
MA0072.10.0898
MA0073.10.368
MA0074.10.134
MA0076.10.643
MA0077.10.732
MA0078.10.608
MA0079.20.225
MA0080.20.905
MA0081.10.499
MA0083.10.00411
MA0084.10.42
MA0087.10.112
MA0088.10.104
MA0090.10.0647
MA0091.10.00164
MA0092.10.19
MA0093.10.264
MA0099.20.853
MA0100.10.0513
MA0101.10.983
MA0102.20.0779
MA0103.15.97306e-6
MA0104.20.337
MA0105.10.854
MA0106.10.135
MA0107.10.438
MA0108.20.134
MA0111.10.706
MA0112.26.03656e-4
MA0113.10.857
MA0114.10.201
MA0115.10.802
MA0116.10.62
MA0117.10.383
MA0119.10.63
MA0122.10.83
MA0124.10.356
MA0125.10.377
MA0131.10.751
MA0135.10.49
MA0136.10.11
MA0137.20.0022
MA0138.20.498
MA0139.10.292
MA0140.10.0199
MA0141.10.0131
MA0142.10.888
MA0143.10.845
MA0144.10.0181
MA0145.10.0217
MA0146.10.0508
MA0147.10.117
MA0148.12.54975e-5
MA0149.10.0194
MA0150.10.286
MA0152.10.845
MA0153.12.68906e-4
MA0154.10.0332
MA0155.10.376
MA0156.10.868
MA0157.10.132
MA0159.10.0921
MA0160.10.113
MA0162.10.52
MA0163.10.0659
MA0164.10.43
MA0258.10.0177
MA0259.10.78



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: CNhs11182

Novel motifP-value
10.06
100.153
1000.523
1010.722
1020.432
1030.0428
1040.436
1050.802
1060.0256
1070.216
1080.899
1090.0556
110.0793
1100.0788
1110.0258
1120.164
1130.561
1140.119
1150.865
1160.205
1170.171
1180.908
1190.027
120.614
1200.975
1210.52
1220.186
1230.718
1240.87
1250.327
1260.0324
1270.44
1280.0115
1290.253
130.00918
1300.9
1310.35
1320.871
1330.0952
1340.781
1350.424
1360.145
1370.169
1380.106
1390.427
140.725
1400.132
1410.508
1420.289
1430.278
1440.445
1450.0393
1460.399
1470.526
1480.221
1490.191
150.278
1500.298
1510.42
1520.00421
1530.689
1540.982
1550.19
1560.698
1570.181
1580.175
1590.631
1600.229
1610.454
1620.714
1630.688
1640.0546
1650.0595
1660.149
1670.709
1680.726
1690.0328
170.0317
180.725
190.0893
20.4
200.833
210.842
220.314
230.525
240.101
250.862
260.0112
270.609
280.77
290.256
30.198
300.913
310.289
320.295
330.626
340.917
350.309
360.46
370.0602
380.48
390.437
40.13
400.682
410.515
420.194
430.386
440.36
450.716
460.104
470.368
480.251
490.215
50.269
500.715
510.607
520.292
530.833
540.735
550.0386
560.467
570.651
580.356
590.0337
60.9
600.103
610.254
620.278
630.101
640.442
650.152
660.253
670.856
680.886
690.226
70.129
700.0661
710.0137
720.341
730.00777
740.632
750.276
760.918
770.063
780.192
790.0535
80.0686
800.882
810.378
820.148
830.696
840.892
850.0342
860.11
870.0278
880.951
890.659
90.712
900.02
910.408
920.131
930.166
940.867
950.388
960.327
970.00766
980.777
990.673



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: CNhs11182


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000160 (intestine)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001045 (midgut)
0001048 (primordium)
0001062 (anatomical entity)
0001264 (pancreas)
0001555 (digestive tract)
0002050 (embryonic structure)
0002075 (viscus)
0002100 (trunk)
0002108 (small intestine)
0002114 (duodenum)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003921 (pancreas primordium)
0003922 (pancreatic epithelial bud)
0003923 (dorsal pancreatic bud)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004458 (body cavity or lining)
0004921 (subdivision of digestive tract)
0005177 (trunk region element)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)

FF: FANTOM5
NA

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
NA

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