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|is_obsolete=
|is_obsolete=
|library_id=CNhs12532
|library_id=CNhs12532
|library_ids=CNhs12532
|name=Sox2+ Supporting cells - organ of corti, pool1
|name=Sox2+ Supporting cells - organ of corti, pool1
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 12:24, 25 October 2013


Name:Sox2+ Supporting cells - organ of corti, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs12532
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueorgan of corti
dev stageNA
sexmixed
ageNA
cell typeSELECT CELL TYPE
cell lineNA
companyNA
collaborationAlbert Edge (Department of Otolaryngology, Harvard Medical School)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008668
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12532 CAGE DRX008778 DRR009650
Accession ID Mm9

Library idBAMCTSS
CNhs12532 DRZ001075 DRZ002460
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

CNhs12532

00
10.0637
100
1000
10000
1001-0.0749
10020.464
1003-0.132
10040
1005-0.0389
10060.0334
10070.205
10080
10090.0414
101-0.0684
10100
10110.0866
10120
10130.0777
1014-0.0874
10150.223
10160.296
10170
10180
10190
1020
10200
10210
10220.0125
10230
10240
10250
10260
10270.517
10280
1029-0.12
103-0.0721
10300
10310
10320.325
10330.0572
10340
10350.0572
10360.0124
10370.0572
10380.0456
1039-0.0717
1040
1040-0.121
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: CNhs12532

Jaspar motifP-value
MA0002.20.00452
MA0003.10.519
MA0004.10.589
MA0006.10.968
MA0007.10.454
MA0009.10.279
MA0014.10.0981
MA0017.12.11564e-9
MA0018.23.08379e-4
MA0019.10.499
MA0024.10.88
MA0025.10.868
MA0027.10.846
MA0028.10.472
MA0029.10.335
MA0030.10.678
MA0031.10.429
MA0035.20.0626
MA0038.10.245
MA0039.20.192
MA0040.10.241
MA0041.10.142
MA0042.10.909
MA0043.10.00496
MA0046.15.32088e-11
MA0047.20.00932
MA0048.10.509
MA0050.10.016
MA0051.10.0497
MA0052.10.138
MA0055.10.955
MA0057.10.475
MA0058.10.845
MA0059.10.152
MA0060.16.62129e-10
MA0061.10.0128
MA0062.20.868
MA0065.22.22353e-4
MA0066.10.0269
MA0067.10.148
MA0068.10.0987
MA0069.10.303
MA0070.10.508
MA0071.10.0929
MA0072.10.584
MA0073.10.88
MA0074.10.08
MA0076.10.289
MA0077.10.0131
MA0078.10.803
MA0079.20.0789
MA0080.23.95037e-10
MA0081.10.252
MA0083.10.0592
MA0084.10.0888
MA0087.10.0555
MA0088.10.259
MA0090.10.216
MA0091.10.31
MA0092.10.413
MA0093.10.709
MA0099.20.0164
MA0100.10.835
MA0101.10.105
MA0102.20.696
MA0103.10.975
MA0104.20.292
MA0105.11.30973e-6
MA0106.10.0487
MA0107.10.0395
MA0108.20.855
MA0111.10.905
MA0112.21.69995e-5
MA0113.10.795
MA0114.18.47883e-6
MA0115.17.88156e-5
MA0116.15.11268e-5
MA0117.10.97
MA0119.10.14
MA0122.10.93
MA0124.10.412
MA0125.10.0233
MA0131.10.711
MA0135.10.155
MA0136.11.90304e-7
MA0137.20.612
MA0138.20.204
MA0139.10.186
MA0140.10.00195
MA0141.10.00473
MA0142.10.782
MA0143.10.0607
MA0144.10.214
MA0145.10.123
MA0146.10.897
MA0147.10.185
MA0148.10.00202
MA0149.10.783
MA0150.10.0272
MA0152.10.81
MA0153.16.33411e-8
MA0154.10.00328
MA0155.10.843
MA0156.11.57498e-4
MA0157.10.326
MA0159.16.00836e-4
MA0160.10.0112
MA0162.10.204
MA0163.12.04606e-4
MA0164.10.47
MA0258.10.00148
MA0259.10.569



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: CNhs12532

Novel motifP-value
10.0367
100.0255
1000.894
1010.642
1020.593
1030.106
1040.646
1050.641
1060.158
1070.219
1080.653
1090.163
110.154
1100.0227
1116.99748e-4
1120.0122
1130.984
1140.00894
1150.89
1160.571
1170.0453
1180.617
1190.0613
120.995
1200.497
1210.589
1220.934
1230.895
1240.817
1250.143
1260.588
1270.333
1280.105
1290.0973
130.0771
1300.267
1310.858
1320.536
1330.845
1340.29
1350.249
1360.331
1370.195
1380.657
1390.0567
140.991
1400.2
1410.733
1420.238
1430.355
1440.693
1450.113
1460.364
1470.566
1480.254
1490.515
150.113
1500.423
1510.388
1520.977
1530.161
1540.452
1550.579
1560.0133
1570.507
1580.421
1590.0137
1600.195
1610.66
1620.64
1630.313
1640.00284
1650.944
1660.795
1670.163
1680.957
1690.00501
170.16
180.176
190.0922
20.811
200.548
210.207
220.418
230.115
240.951
250.453
260.0134
270.876
280.624
290.0573
30.0537
300.94
310.584
320.0435
330.586
340.931
350.161
360.104
370.149
380.269
390.825
40.28
400.811
410.678
420.0696
430.0928
440.618
450.927
460.0207
470.272
480.26
490.0939
50.198
500.664
510.518
520.901
530.854
540.697
550.847
560.257
570.502
580.287
590.0423
60.891
600.4
610.317
620.118
630.107
640.301
650.144
660.268
670.648
680.00706
690.661
70.177
700.0177
710.0148
720.578
730.541
740.227
750.0597
760.428
770.344
780.00275
790.833
80.101
800.842
810.505
820.0987
830.476
840.615
850.0506
860.622
870.0253
880.944
890.128
90.345
900.0573
910.219
920.185
930.231
940.32
950.385
960.226
970.795
980.373
990.339



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: CNhs12532


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)
0000197 (receptor cell)
0000003 (native cell)
0000548 (animal cell)
0000075 (columnar/cuboidal epithelial cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000710 (neurecto-epithelial cell)
0002491 (auditory epithelial cell)
0000630 (supportive cell)
0000255 (eukaryotic cell)
0002077 (ecto-epithelial cell)
0000098 (sensory epithelial cell)
0005014 (auditory epithelial support cell)
0002315 (supporting cell of cochlea)
0002490 (organ of Corti supporting cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001474 (bone element)
0000033 (head)
0000058 (duct)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0000075 (subdivision of skeletal system)
0004765 (skeletal element)
0004766 (cranial bone)
0008193 (pneumatized bone)
0005913 (zone of bone organ)
0005744 (cranial conduit)
0001032 (sensory system)
0003457 (head bone)
0008001 (irregular bone)
0007914 (head or neck bone)
0010317 (germ layer / neural crest derived structure)
0002227 (spiral organ of cochlea)
0001846 (internal ear)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0004456 (entire sense organ system)
0004339 (calvarium)
0002105 (vestibulo-auditory system)
0001678 (temporal bone)
0003128 (cranium)
0001694 (petrous part of temporal bone)
0004681 (vestibular system)
0001839 (bony labyrinth)
0001690 (ear)
0001844 (cochlea)
0001849 (membranous labyrinth)
0002499 (cochlear labyrinth)
0001855 (cochlear duct of membranous labyrinth)
0011137 (axial skeletal system)
0010323 (cranial skeletal system)
0003129 (skull)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000279 (mouse Sox2-positive supporting cell- organ of corti 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:0000133 (neurectodermal cell)
CL:0000221 (ectodermal cell)

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