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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:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001062,UBERON:0002050,UBERON:0002410,UBERON:0002532,UBERON:0004121,UBERON:0005423
|ancestors_in_anatomy_facet=UBERON:0000010,UBERON:0000013,UBERON:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001062,UBERON:0002050,UBERON:0002410,UBERON:0002532,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:0100932
|fonse_cell_line=FF:0100932
|fonse_cell_line_closure=FF:0100932
|fonse_cell_line_closure=FF:0100932

Revision as of 16:42, 29 March 2012


Name:neuroblastoma cell line:CHP-134
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueadrenal gland
dev stageNA
sexunknown
ageNA
cell typeneuroblast
cell lineCHP-134
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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-Neural0.0523
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-penis0.0839
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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: CNhs11276

Jaspar motifP-value
MA0002.24.14918e-6
MA0003.10.198
MA0004.10.395
MA0006.10.0999
MA0007.10.12
MA0009.10.21
MA0014.10.665
MA0017.18.30285e-4
MA0018.20.00817
MA0019.10.184
MA0024.12.26926e-4
MA0025.10.466
MA0027.10.981
MA0028.10.0467
MA0029.10.708
MA0030.10.971
MA0031.10.433
MA0035.20.899
MA0038.11.95869e-4
MA0039.20.0737
MA0040.10.342
MA0041.10.334
MA0042.10.714
MA0043.10.0286
MA0046.10.378
MA0047.20.0195
MA0048.10.933
MA0050.11.24946e-10
MA0051.12.20328e-4
MA0052.10.31
MA0055.10.868
MA0057.10.0765
MA0058.10.365
MA0059.10.3
MA0060.12.54428e-12
MA0061.10.00831
MA0062.20.027
MA0065.20.00423
MA0066.10.0529
MA0067.10.898
MA0068.10.0536
MA0069.10.92
MA0070.10.134
MA0071.10.468
MA0072.10.962
MA0073.10.545
MA0074.10.152
MA0076.17.86667e-4
MA0077.10.183
MA0078.10.57
MA0079.20.521
MA0080.23.43318e-11
MA0081.10.134
MA0083.10.0015
MA0084.10.23
MA0087.10.251
MA0088.10.516
MA0090.10.0131
MA0091.10.133
MA0092.10.268
MA0093.10.295
MA0099.21.38576e-15
MA0100.10.261
MA0101.10.0189
MA0102.20.341
MA0103.10.174
MA0104.20.0938
MA0105.10.032
MA0106.10.315
MA0107.10.00521
MA0108.20.00205
MA0111.10.906
MA0112.21.95401e-4
MA0113.10.0505
MA0114.10.0158
MA0115.10.831
MA0116.10.017
MA0117.10.72
MA0119.10.0983
MA0122.10.304
MA0124.10.695
MA0125.10.242
MA0131.10.341
MA0135.10.541
MA0136.11.37956e-7
MA0137.20.207
MA0138.20.912
MA0139.10.406
MA0140.10.784
MA0141.10.0432
MA0142.10.59
MA0143.10.475
MA0144.10.00818
MA0145.10.0803
MA0146.10.0584
MA0147.10.105
MA0148.10.0348
MA0149.10.0689
MA0150.14.23781e-4
MA0152.10.778
MA0153.10.216
MA0154.10.0315
MA0155.10.366
MA0156.10.00673
MA0157.10.109
MA0159.10.00816
MA0160.10.151
MA0162.10.201
MA0163.10.00929
MA0164.10.944
MA0258.10.00851
MA0259.10.159



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: CNhs11276

Novel motifP-value
10.302
100.216
1000.929
1010.991
1020.599
1030.0844
1040.39
1050.661
1060.00314
1070.00565
1080.66
1090.0191
110.12
1100.301
1110.723
1120.0655
1130.78
1140.0327
1150.222
1160.342
1170.241
1180.39
1190.318
120.468
1200.0551
1210.906
1220.604
1230.0548
1240.24
1250.974
1260.117
1270.352
1280.0336
1290.261
130.0898
1300.833
1310.399
1320.727
1330.897
1340.619
1350.275
1360.227
1370.289
1380.771
1390.391
140.605
1400.245
1410.467
1420.841
1430.165
1440.561
1450.121
1460.733
1470.331
1480.0339
1490.0695
150.211
1500.233
1510.429
1520.0554
1530.777
1540.952
1550.736
1560.818
1570.236
1580.419
1590.0934
160.0996
1600.12
1610.71
1620.741
1630.16
1640.0731
1650.289
1660.43
1670.741
1680.0281
1690.0147
170.141
180.552
190.0798
20.246
200.962
210.533
220.0888
230.00223
240.162
250.662
260.06
270.265
280.902
290.148
30.141
300.311
310.485
320.00605
330.198
340.551
350.944
360.653
370.126
380.231
390.071
40.364
400.234
410.292
420.73
430.142
440.0662
450.376
460.209
470.525
480.313
490.405
50.161
500.45
510.456
520.0976
530.839
540.31
550.127
560.484
570.834
580.212
590.0309
60.927
600.0105
610.336
620.0945
630.153
640.836
650.13
660.171
670.63
680.75
690.567
70.226
700.0153
710.0734
720.124
730.0288
740.709
750.312
760.963
770.0391
780.125
790.0889
80.153
800.142
810.385
820.0989
830.155
840.435
850.0341
860.567
870.185
880.705
890.0258
90.183
900.701
910.34
920.082
930.873
940.29
950.0952
960.418
970.737
980.339
990.241



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: CNhs11276


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
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
169 (neuroendocrine tumor)
171 (neuroectodermal tumor)
2994 (germ cell cancer)
3095 (germ cell and embryonal cancer)
4 (disease)

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)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002410 (autonomic nervous system)
0002532 (epiblast (generic))
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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