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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000010,UBERON:0000013,UBERON:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001062,UBERON:0002050,UBERON:0002384,UBERON:0002410,UBERON:0002532,UBERON:0003714,UBERON:0004121,UBERON:0005423
|ancestors_in_anatomy_facet=UBERON:0000010,UBERON:0000013,UBERON:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001062,UBERON:0002050,UBERON:0002384,UBERON:0002410,UBERON:0002532,UBERON:0003714,UBERON:0004121,UBERON:0005423
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000255,CL:0000333,CL:0000548,CL:0002321
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000255,CL:0000333,CL:0000548,CL:0002321
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100400,FF:0100932,FF:0102912
|fonse_cell_line=FF:0100400,FF:0100932,FF:0102912
|fonse_cell_line_closure=FF:0100400,FF:0100932,FF:0102912
|fonse_cell_line_closure=FF:0100400,FF:0100932,FF:0102912

Revision as of 16:56, 29 March 2012


Name:neuroepithelioma cell line:SK-N-MC
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexfemale
age14
cell typeunclassifiable
cell lineSK-N-MC
companyATCC
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} 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

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



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: CNhs11853

Jaspar motifP-value
MA0002.20.00894
MA0003.10.34
MA0004.10.00807
MA0006.10.0364
MA0007.10.634
MA0009.10.076
MA0014.10.476
MA0017.10.0033
MA0018.20.0271
MA0019.10.802
MA0024.12.3308e-8
MA0025.10.742
MA0027.10.231
MA0028.10.629
MA0029.10.141
MA0030.10.787
MA0031.10.575
MA0035.20.279
MA0038.10.0228
MA0039.20.394
MA0040.10.528
MA0041.10.322
MA0042.10.973
MA0043.10.149
MA0046.10.444
MA0047.20.698
MA0048.10.538
MA0050.18.06653e-17
MA0051.11.09648e-5
MA0052.10.265
MA0055.10.0982
MA0057.10.904
MA0058.10.0115
MA0059.10.055
MA0060.11.04766e-8
MA0061.10.181
MA0062.20.604
MA0065.20.0274
MA0066.10.0938
MA0067.10.296
MA0068.18.8273e-4
MA0069.10.168
MA0070.10.206
MA0071.10.963
MA0072.10.301
MA0073.10.681
MA0074.10.348
MA0076.10.287
MA0077.10.381
MA0078.10.599
MA0079.20.558
MA0080.25.61521e-10
MA0081.10.0419
MA0083.10.0565
MA0084.10.0404
MA0087.10.768
MA0088.10.303
MA0090.10.653
MA0091.10.395
MA0092.10.249
MA0093.10.00385
MA0099.22.58416e-9
MA0100.10.531
MA0101.10.5
MA0102.20.0771
MA0103.10.205
MA0104.20.0014
MA0105.10.252
MA0106.10.233
MA0107.10.401
MA0108.20.907
MA0111.10.907
MA0112.22.85935e-4
MA0113.10.34
MA0114.10.0294
MA0115.10.368
MA0116.10.208
MA0117.10.707
MA0119.10.717
MA0122.10.712
MA0124.10.829
MA0125.10.651
MA0131.10.642
MA0135.10.992
MA0136.19.90891e-6
MA0137.20.955
MA0138.20.367
MA0139.10.626
MA0140.10.88
MA0141.10.407
MA0142.10.171
MA0143.10.251
MA0144.10.141
MA0145.10.00322
MA0146.10.311
MA0147.10.00172
MA0148.10.766
MA0149.10.00147
MA0150.10.00628
MA0152.10.386
MA0153.10.863
MA0154.10.252
MA0155.10.635
MA0156.10.0793
MA0157.10.369
MA0159.12.29328e-4
MA0160.10.313
MA0162.10.0783
MA0163.10.295
MA0164.10.975
MA0258.10.0476
MA0259.10.0115



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: CNhs11853

Novel motifP-value
10.664
100.267
1000.82
1010.768
1020.74
1030.0746
1040.874
1050.688
1068.98929e-4
1070.0147
1080.478
1090.0822
110.215
1100.778
1110.302
1120.00518
1130.445
1140.00562
1150.0897
1160.34
1170.614
1180.283
1190.146
120.526
1200.744
1210.295
1220.386
1230.416
1240.589
1250.588
1260.443
1270.503
1280.129
1290.705
130.781
1300.019
1310.28
1320.488
1330.285
1340.451
1350.0895
1360.502
1370.191
1380.634
1390.452
140.27
1400.0312
1410.164
1420.995
1430.335
1440.389
1450.0963
1460.919
1470.955
1480.0678
1490.0483
150.824
1500.286
1510.169
1520.0163
1530.923
1540.891
1550.222
1560.892
1570.259
1580.374
1590.282
160.15
1600.441
1610.745
1620.472
1630.924
1640.28
1650.918
1660.313
1670.735
1680.328
1690.0071
170.523
180.664
190.0121
20.123
200.811
210.0911
220.238
230.144
240.853
250.407
260.203
270.326
280.713
290.444
30.277
300.671
310.308
328.29642e-5
330.642
340.818
350.749
360.464
370.0313
380.472
390.237
40.2
400.439
410.353
420.468
430.32
440.133
450.428
460.173
470.457
480.454
490.716
50.309
500.265
510.577
520.144
530.55
540.506
550.484
560.623
570.411
580.481
590.0546
60.7
600.0644
610.468
620.321
630.352
640.978
650.356
660.222
670.283
680.62
690.522
70.979
700.00694
710.0492
720.521
730.00657
740.962
750.241
760.963
770.0282
780.456
790.022
80.707
800.5
810.653
820.159
830.167
840.501
851.7935e-4
860.4
870.168
880.622
890.105
90.381
900.952
910.171
920.137
930.871
940.455
950.156
960.771
970.336
980.765
990.513



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: CNhs11853


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)
0000133 (neurectodermal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000333 (migratory neural crest cell)
0000548 (animal cell)
0002321 (embryonic cell)

DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
1115 (sarcoma)
1192 (peripheral nervous system neoplasm)
14566 (disease of cellular proliferation)
162 (cancer)
169 (neuroendocrine tumor)
171 (neuroectodermal tumor)
2994 (germ cell cancer)
3093 (nervous system cancer)
3095 (germ cell and embryonal cancer)
3193 (peripheral nerve sheath neoplasm)
4 (disease)
962 (neurofibroma)

UBERON: Anatomy
0000010 (peripheral nervous system)
0000013 (sympathetic nervous system)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002384 (connective tissue)
0002410 (autonomic nervous system)
0002532 (epiblast (generic))
0003714 (neural tissue)
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)

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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