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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000349,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0000956,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001869,UBERON:0001890,UBERON:0001893,UBERON:0001954,UBERON:0002050,UBERON:0002346,UBERON:0002421,UBERON:0002532,UBERON:0002600,UBERON:0002616,UBERON:0002619,UBERON:0002780,UBERON:0002791,UBERON:0003022,UBERON:0003056,UBERON:0003075,UBERON:0003080,UBERON:0004121,UBERON:0005068,UBERON:0005291,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007135,UBERON:0007284
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0000483,UBERON:0001954,UBERON:0000956,UBERON:0000033,UBERON:0000479,UBERON:0002346,UBERON:0000064,UBERON:0000073,UBERON:0004121,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000025,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000477,UBERON:0002020,UBERON:0002791,UBERON:0003528,UBERON:0000481,UBERON:0000467,UBERON:0002616,UBERON:0002619,UBERON:0001062,UBERON:0000119,UBERON:0005291,UBERON:0002780,UBERON:0003022,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0002421,UBERON:0001016,UBERON:0000153,UBERON:0007811,UBERON:0000924,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0005743,UBERON:0000349,UBERON:0002600,UBERON:0003075,UBERON:0003056,UBERON:0001049,UBERON:0006238,UBERON:0006601,UBERON:0005068,UBERON:0006241,UBERON:0003080,UBERON:0006240,UBERON:0007284,UBERON:0007135
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000031,CL:0000034,CL:0000047,CL:0000048,CL:0000055,CL:0000117,CL:0000133,CL:0000144,CL:0000211,CL:0000220,CL:0000221,CL:0000255,CL:0000337,CL:0000393,CL:0000404,CL:0000540,CL:0000548,CL:0000723,CL:0002319,CL:0002321,CL:0002371,CL:0002608
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000540,CL:0000055,CL:0000047,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0002321,CL:0002371,CL:0002319,CL:0000221,CL:0000117,CL:0000393,CL:0000220,CL:0000004,CL:0000031,CL:0000211,CL:0000404,CL:0000255,CL:0002608,CL:0002609,CL:0000133,CL:0000337
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|comment=
|comment=

Revision as of 17:19, 8 June 2012


Name:Mouse Neurons - hippocampal, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuehippocampus
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMNh1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
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

CNhs12133

00
10.238
100
1000.568
1000-0.0104
1001-0.0498
10020.202
10030.0522
10040.0251
1005-0.184
10060.158
10070.00165
10080
1009-0.2
101-0.0723
10100
10110.1
10120.0446
1013-0.16
10140
10150.433
10160.034
10170
10180
10190
1020
10200.568
10210.191
1022-0.124
10230
1024-0.171
1025-0.0611
10260
10270.489
10280
1029-0.148
103-0.0861
10300
1031-0.529
1032-0.177
1033-0.025
10340
10350
1036-0.0877
10370
10380.0726
1039-0.233
1040
1040-0.216
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 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: CNhs12133

Jaspar motifP-value
MA0002.20.00226
MA0003.10.126
MA0004.10.882
MA0006.10.0885
MA0007.10.197
MA0009.10.961
MA0014.10.374
MA0017.12.03512e-5
MA0018.20.0114
MA0019.10.263
MA0024.10.015
MA0025.10.299
MA0027.10.647
MA0028.10.878
MA0029.10.513
MA0030.10.383
MA0031.10.06
MA0035.20.11
MA0038.10.0134
MA0039.20.0108
MA0040.10.857
MA0041.10.215
MA0042.10.476
MA0043.10.0162
MA0046.11.8521e-9
MA0047.26.1223e-4
MA0048.10.673
MA0050.11.0469e-8
MA0051.10.00106
MA0052.10.00618
MA0055.10.8
MA0057.10.0552
MA0058.10.819
MA0059.10.757
MA0060.12.36763e-9
MA0061.10.05
MA0062.20.783
MA0065.23.85793e-5
MA0066.10.187
MA0067.10.849
MA0068.10.303
MA0069.10.0814
MA0070.10.552
MA0071.10.23
MA0072.10.238
MA0073.10.921
MA0074.10.337
MA0076.10.289
MA0077.10.00344
MA0078.10.00582
MA0079.20.761
MA0080.29.09905e-11
MA0081.10.448
MA0083.11.07457e-5
MA0084.10.529
MA0087.10.58
MA0088.10.401
MA0090.10.0099
MA0091.10.409
MA0092.10.21
MA0093.10.882
MA0099.28.14343e-5
MA0100.10.651
MA0101.10.136
MA0102.20.731
MA0103.10.0705
MA0104.20.356
MA0105.10.0833
MA0106.10.155
MA0107.10.0761
MA0108.20.00877
MA0111.10.889
MA0112.22.70533e-4
MA0113.10.525
MA0114.11.30914e-4
MA0115.10.0425
MA0116.10.112
MA0117.10.838
MA0119.10.132
MA0122.10.914
MA0124.10.929
MA0125.10.133
MA0131.10.556
MA0135.10.36
MA0136.14.65355e-7
MA0137.20.0521
MA0138.20.741
MA0139.10.224
MA0140.10.00723
MA0141.10.0089
MA0142.10.00167
MA0143.19.53859e-4
MA0144.10.0485
MA0145.10.0261
MA0146.10.0496
MA0147.10.415
MA0148.11.55932e-5
MA0149.10.092
MA0150.10.0658
MA0152.10.381
MA0153.11.94808e-8
MA0154.10.0209
MA0155.10.629
MA0156.12.94742e-4
MA0157.10.0198
MA0159.10.00361
MA0160.10.0914
MA0162.10.277
MA0163.10.00775
MA0164.10.935
MA0258.10.00965
MA0259.10.403



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: CNhs12133

Novel motifP-value
10.179
100.203
1000.995
1010.955
1020.796
1030.073
1040.933
1050.229
1060.00517
1070.0281
1080.666
1090.00285
110.0766
1100.146
1110.0265
1120.00372
1130.992
1140.13
1150.279
1160.557
1170.198
1180.474
1190.144
120.477
1200.963
1210.285
1220.662
1230.584
1240.567
1250.505
1260.205
1270.102
1280.0142
1290.0992
133.42542e-5
1300.775
1310.532
1320.756
1330.228
1340.488
1350.208
1360.0773
1370.335
1380.579
1390.151
140.606
1400.398
1410.12
1420.23
1430.812
1440.859
1450.0425
1460.439
1470.965
1480.5
1490.0465
150.194
1500.199
1510.388
1520.0289
1530.961
1540.989
1550.384
1560.00409
1570.168
1580.301
1590.0178
1600.228
1610.368
1620.752
1630.167
1640.0254
1650.0132
1660.618
1670.572
1680.729
1690.00697
170.021
180.772
190.0375
20.506
200.869
210.546
220.0664
230.181
240.0365
250.841
260.00123
270.671
280.432
290.314
30.0964
300.519
310.701
320.225
330.283
340.534
350.521
360.917
370.00977
380.348
390.152
40.569
400.289
410.856
420.355
430.142
440.54
450.38
460.184
470.194
480.161
490.175
50.192
500.226
510.581
520.0756
530.634
540.579
550.921
560.305
570.717
580.306
590.0604
60.628
600.00987
610.267
620.163
630.106
640.927
650.28
660.572
670.711
680.447
690.379
70.0393
700.013
710.0394
720.382
730.0136
740.339
750.131
760.851
770.138
780.0383
790.611
80.222
800.865
810.374
820.0302
830.0992
840.866
850.0303
860.304
870.338
880.347
890.318
90.315
900.409
910.27
920.117
930.0364
940.93
950.0444
960.314
970.876
980.701
990.168



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: CNhs12133


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)
0000540 (neuron)
0000055 (non-terminally differentiated cell)
0000047 (neuronal stem cell)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0000034 (stem cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002319 (neural cell)
0000221 (ectodermal cell)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000031 (neuroblast)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0002608 (hippocampal neuron)
0002609 (neuron of cerebral cortex)
0000133 (neurectodermal cell)
0000337 (neuroblast (sensu Vertebrata))

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000955 (brain)
0000483 (epithelium)
0001954 (Ammon's horn)
0000956 (cerebral cortex)
0000033 (head)
0000479 (tissue)
0002346 (neurectoderm)
0000064 (organ part)
0000073 (regional part of nervous system)
0004121 (ectoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000025 (tube)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0000477 (anatomical cluster)
0002020 (gray matter)
0002791 (regional part of telencephalon)
0003528 (brain grey matter)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0002616 (regional part of brain)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000119 (cell layer)
0005291 (embryonic tissue)
0002780 (regional part of forebrain)
0003022 (lobe parts of cerebral cortex)
0006598 (presumptive structure)
0002532 (epiblast (generic))
0001017 (central nervous system)
0002421 (hippocampal formation)
0001016 (nervous system)
0000153 (anterior region of body)
0007811 (craniocervical region)
0000924 (ectoderm)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0000349 (limbic system)
0002600 (limbic lobe)
0003075 (neural plate)
0003056 (pre-chordal neural plate)
0001049 (neural tube)
0006238 (future brain)
0006601 (presumptive ectoderm)
0005068 (neural rod)
0006241 (future spinal cord)
0003080 (anterior neural tube)
0006240 (future forebrain)
0007284 (presumptive neural plate)
0007135 (neural keel)

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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