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FF:13-16E8

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Name:hippocampus, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10478
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuehippocampus
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005812
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10478 CAGE DRX008986 DRR009860
Accession ID Mm9

Library idBAMCTSS
CNhs10478 DRZ001285 DRZ002668
Accession ID Mm10

Library idBAMCTSS
CNhs10478 DRZ012635 DRZ014018
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

CNhs10478

00
10.782
100
1000
1000-0.0205
10010.0406
1002-0.0856
10030.26
10040
10050.106
10060.575
1007-0.0278
10080
1009-0.162
101-0.036
10100
10110.835
10120.265
10130.12
1014-0.0874
1015-0.0888
1016-0.227
10170
10180
10190
1020
10200
10210
10220.0285
10230
10240.0129
10250
10260
10270.368
10280
10290.172
103-0.0848
10300
1031-0.476
10320.227
10330.0312
10340
10350
1036-0.195
10370
1038-0.0319
10390.152
1040
1040-0.163
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: CNhs10478

Jaspar motifP-value
MA0002.20.00627
MA0003.10.324
MA0004.10.533
MA0006.10.133
MA0007.10.568
MA0009.10.482
MA0014.10.716
MA0017.16.27848e-7
MA0018.20.0256
MA0019.10.278
MA0024.10.0251
MA0025.10.00664
MA0027.10.053
MA0028.10.093
MA0029.10.861
MA0030.10.419
MA0031.10.268
MA0035.20.0235
MA0038.10.415
MA0039.20.0324
MA0040.10.332
MA0041.10.0624
MA0042.10.168
MA0043.10.109
MA0046.19.59254e-10
MA0047.21.66036e-4
MA0048.10.0675
MA0050.12.8484e-4
MA0051.10.0516
MA0052.10.832
MA0055.10.0229
MA0057.10.437
MA0058.10.422
MA0059.10.163
MA0060.10.759
MA0061.10.0351
MA0062.20.00471
MA0065.26.75888e-7
MA0066.10.0147
MA0067.10.689
MA0068.10.732
MA0069.10.0585
MA0070.10.271
MA0071.10.0267
MA0072.10.138
MA0073.10.997
MA0074.10.108
MA0076.10.247
MA0077.10.301
MA0078.10.683
MA0079.20.338
MA0080.22.12652e-9
MA0081.10.362
MA0083.10.015
MA0084.10.835
MA0087.10.236
MA0088.10.44
MA0090.10.218
MA0091.10.219
MA0092.10.247
MA0093.10.587
MA0099.20.00273
MA0100.10.291
MA0101.10.0174
MA0102.20.475
MA0103.10.126
MA0104.20.885
MA0105.10.00894
MA0106.10.0592
MA0107.10.0339
MA0108.20.00152
MA0111.10.967
MA0112.25.47942e-4
MA0113.10.461
MA0114.16.3393e-6
MA0115.16.27948e-5
MA0116.10.0737
MA0117.10.907
MA0119.10.125
MA0122.10.96
MA0124.10.396
MA0125.10.0247
MA0131.10.741
MA0135.10.352
MA0136.13.96042e-11
MA0137.20.141
MA0138.26.55491e-4
MA0139.10.598
MA0140.11.98063e-4
MA0141.13.16374e-4
MA0142.10.486
MA0143.10.716
MA0144.10.101
MA0145.10.127
MA0146.10.0161
MA0147.10.762
MA0148.19.25497e-5
MA0149.10.126
MA0150.10.131
MA0152.10.213
MA0153.13.38615e-10
MA0154.10.0479
MA0155.10.355
MA0156.13.29603e-7
MA0157.10.0874
MA0159.10.00109
MA0160.10.00189
MA0162.10.143
MA0163.13.08128e-4
MA0164.10.788
MA0258.10.0162
MA0259.10.923



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: CNhs10478

Novel motifP-value
10.194
100.0504
1000.375
1010.676
1020.912
1030.0492
1040.896
1050.82
1060.0421
1070.22
1080.66
1090.00571
110.0702
1100.0497
1110.106
1120.00365
1130.44
1140.386
1150.948
1160.22
1170.0041
1180.373
1190.215
120.872
1200.893
1210.423
1220.715
1230.00317
1240.066
1250.144
1260.0209
1270.32
1280.0266
1290.265
134.82902e-7
1300.12
1310.64
1320.761
1330.993
1340.0962
1350.243
1360.064
1370.714
1380.855
1390.402
140.959
1400.0131
1410.585
1420.698
1430.223
1440.877
1459.41431e-4
1460.504
1470.264
1480.613
1490.621
150.223
1500.0485
1510.772
1520.0816
1530.959
1540.99
1550.258
1560.00633
1570.354
1580.115
1590.638
1600.142
1610.0818
1620.515
1630.834
1640.0617
1650.0513
1660.693
1670.834
1680.695
1690.00408
170.0441
180.657
190.0919
20.864
200.0532
210.241
220.143
230.66
240.055
250.756
262.80597e-7
270.616
280.654
290.035
30.0411
300.715
310.944
320.514
330.202
340.78
350.931
360.348
370.0276
380.508
390.249
40.143
400.127
410.51
420.187
430.138
440.33
450.754
460.103
470.386
480.341
490.228
50.167
500.214
510.734
520.25
530.443
540.901
550.921
560.488
570.764
580.305
590.098
60.948
600.0364
610.0388
620.258
630.162
640.677
650.415
660.695
670.6
680.858
690.312
70.0207
700.105
710.00597
720.604
730.0269
740.861
750.044
760.473
770.342
780.00159
790.991
80.0731
800.472
810.974
820.232
830.165
840.933
850.202
860.184
870.197
880.468
890.796
90.509
900.136
910.0822
920.229
930.0711
940.72
950.0212
960.426
970.868
980.564
990.37



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: CNhs10478


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)
0000955 (brain)
0001954 (Ammon's horn)
0000956 (cerebral cortex)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0003022 (lobe parts of cerebral cortex)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002421 (hippocampal formation)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0000349 (limbic system)
0002600 (limbic lobe)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0010153 (hippocampus - 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:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)

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