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FF:1251-16I5

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Name:intestine, embryo E12
Species:Mouse (Mus musculus)
Library ID:CNhs11019
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissueintestine
dev stage12 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  SAMD00004885
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11019 CAGE DRX008990 DRR009864
Accession ID Mm9

Library idBAMCTSS
CNhs11019 DRZ001289 DRZ002672
Accession ID Mm10

Library idBAMCTSS
CNhs11019 DRZ012639 DRZ014022
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11019

00
10
100
1000.0477
10000
1001-0.0275
10020.75
1003-0.156
10040
1005-0.0389
1006-0.11
10070.15
10080
10090.00821
1010.159
10100.084
10110.0175
10120
1013-0.217
10140.551
10150.32
10160.324
10170
10180
10190
1020
10200
10210
10220
10230
10240.0081
10250.843
10260
10270.0933
10280
10290.175
1030.0672
10300
10310.342
1032-0.0536
10330.0867
10340
10350.084
10360.212
10370
1038-0.0714
1039-0.145
1040
10400.125
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: CNhs11019

Jaspar motifP-value
MA0002.22.26863e-4
MA0003.10.134
MA0004.10.777
MA0006.10.277
MA0007.10.384
MA0009.10.384
MA0014.10.351
MA0017.12.65087e-4
MA0018.20.73
MA0019.10.719
MA0024.11.51362e-6
MA0025.15.80579e-5
MA0027.10.0516
MA0028.10.0534
MA0029.10.368
MA0030.10.241
MA0031.10.051
MA0035.20.106
MA0038.10.0711
MA0039.20.00767
MA0040.10.374
MA0041.10.114
MA0042.10.346
MA0043.10.489
MA0046.10.107
MA0047.20.12
MA0048.10.00931
MA0050.11.26772e-5
MA0051.15.44563e-6
MA0052.11.28283e-9
MA0055.10.0149
MA0057.10.0616
MA0058.10.563
MA0059.10.329
MA0060.17.41325e-11
MA0061.10.119
MA0062.20.326
MA0065.21.09072e-4
MA0066.10.054
MA0067.10.376
MA0068.10.771
MA0069.10.726
MA0070.10.881
MA0071.10.0571
MA0072.10.0164
MA0073.10.325
MA0074.10.81
MA0076.10.0492
MA0077.10.284
MA0078.10.592
MA0079.20.0564
MA0080.29.63726e-9
MA0081.10.219
MA0083.10.0359
MA0084.10.554
MA0087.10.538
MA0088.10.911
MA0090.10.895
MA0091.10.922
MA0092.10.702
MA0093.10.762
MA0099.25.96972e-7
MA0100.10.591
MA0101.10.569
MA0102.20.621
MA0103.10.00184
MA0104.20.259
MA0105.10.387
MA0106.10.253
MA0107.10.209
MA0108.20.0379
MA0111.10.658
MA0112.24.79069e-4
MA0113.10.79
MA0114.10.00155
MA0115.10.0846
MA0116.10.247
MA0117.10.0409
MA0119.10.0296
MA0122.10.446
MA0124.10.217
MA0125.10.564
MA0131.10.122
MA0135.10.297
MA0136.13.10422e-4
MA0137.20.264
MA0138.28.01999e-4
MA0139.10.343
MA0140.10.555
MA0141.10.00637
MA0142.10.45
MA0143.10.0161
MA0144.10.258
MA0145.10.0177
MA0146.10.389
MA0147.10.294
MA0148.10.0234
MA0149.10.0771
MA0150.16.25113e-4
MA0152.10.255
MA0153.10.167
MA0154.10.0272
MA0155.10.97
MA0156.10.0999
MA0157.10.0394
MA0159.10.0408
MA0160.10.0136
MA0162.10.95
MA0163.10.888
MA0164.10.685
MA0258.16.84469e-4
MA0259.10.502



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: CNhs11019

Novel motifP-value
10.149
100.853
1000.762
1010.639
1020.617
1030.177
1040.882
1050.161
1060.0101
1070.0724
1080.871
1090.14
110.191
1100.575
1110.265
1120.0841
1130.375
1140.0106
1150.404
1160.461
1170.969
1180.845
1190.031
120.695
1200.83
1210.449
1220.668
1230.0827
1240.291
1250.939
1260.753
1270.0937
1280.0335
1290.0782
130.738
1300.379
1310.144
1320.615
1330.823
1340.447
1350.965
1360.659
1370.946
1380.423
1390.0142
140.321
1400.00305
1410.399
1420.842
1430.846
1440.934
1450.92
1460.216
1470.584
1480.467
1490.186
150.068
1500.616
1510.0793
1520.0349
1530.202
1540.839
1550.935
1560.0134
1570.932
1580.623
1590.322
1600.856
1610.617
1620.767
1630.0887
1640.818
1650.341
1660.0899
1670.321
1680.501
1690.0429
170.12
180.397
190.578
20.444
200.431
210.912
220.295
230.0492
240.393
250.312
260.632
270.259
280.251
290.967
30.477
300.6
310.328
320.327
330.734
340.692
350.458
360.658
370.163
380.317
390.724
40.45
400.383
410.0869
420.824
430.248
440.0619
450.286
460.386
470.197
480.195
490.18
50.126
500.898
510.596
520.321
530.556
540.389
550.774
560.366
570.846
580.304
590.0615
60.754
600.126
610.511
620.0905
630.172
640.498
650.143
660.789
670.703
680.114
690.545
70.31
704.19463e-4
710.672
720.511
730.083
740.888
750.248
760.295
770.162
780.182
790.479
80.282
800.0654
810.338
820.0629
830.537
840.27
850.0062
860.516
870.0507
880.843
890.128
90.424
900.446
910.191
920.188
930.999
940.815
950.0954
960.604
970.769
980.0688
990.984



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: CNhs11019


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0002679 (natural helper lymphocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
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)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000350 (experimentally modified sample)
0000391 (15 days sample)
0000636 (IL-2 treatment sample)
0000295 (mouse embryonic day 12 sample)
0011524 (mouse natural helper cells- IL2 treated, day15 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
CL:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)
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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