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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101533
|fonse_cell_line=FF:0101533
|fonse_cell_line_closure=FF:0101533
|fonse_cell_line_closure=FF:0101533

Revision as of 16:56, 29 March 2012


Name:carcinoid cell line:SK-PN-DW
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueretroperitoneum
dev stageNA
sexmale
age17
cell typeneuroendocrine cell
cell lineSK-PN-DW
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-penis0.214
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.588
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11846

Jaspar motifP-value
MA0002.22.83559e-5
MA0003.10.198
MA0004.10.156
MA0006.10.0271
MA0007.10.215
MA0009.10.37
MA0014.10.745
MA0017.10.012
MA0018.20.141
MA0019.10.0607
MA0024.12.70725e-6
MA0025.10.509
MA0027.10.099
MA0028.10.7
MA0029.10.665
MA0030.10.0624
MA0031.10.0345
MA0035.20.197
MA0038.10.182
MA0039.20.295
MA0040.10.114
MA0041.10.265
MA0042.10.567
MA0043.10.534
MA0046.10.162
MA0047.20.301
MA0048.10.132
MA0050.17.58722e-7
MA0051.15.26263e-4
MA0052.10.118
MA0055.10.381
MA0057.10.235
MA0058.10.158
MA0059.10.0475
MA0060.12.20479e-5
MA0061.10.0507
MA0062.20.293
MA0065.20.0429
MA0066.10.402
MA0067.10.387
MA0068.10.573
MA0069.10.952
MA0070.10.487
MA0071.10.623
MA0072.10.66
MA0073.10.321
MA0074.10.385
MA0076.10.804
MA0077.10.577
MA0078.10.275
MA0079.20.0661
MA0080.23.29198e-9
MA0081.10.0216
MA0083.10.0149
MA0084.10.253
MA0087.10.374
MA0088.10.0843
MA0090.10.0628
MA0091.10.719
MA0092.10.759
MA0093.10.14
MA0099.21.87986e-14
MA0100.10.223
MA0101.10.00504
MA0102.20.00408
MA0103.10.97
MA0104.20.00374
MA0105.10.768
MA0106.10.16
MA0107.10.00183
MA0108.27.38339e-4
MA0111.10.491
MA0112.20.0146
MA0113.10.138
MA0114.10.0681
MA0115.10.803
MA0116.10.994
MA0117.10.558
MA0119.10.226
MA0122.10.178
MA0124.10.945
MA0125.10.807
MA0131.10.356
MA0135.10.0381
MA0136.14.38522e-8
MA0137.20.0364
MA0138.20.607
MA0139.10.841
MA0140.10.351
MA0141.10.389
MA0142.10.869
MA0143.10.539
MA0144.10.00897
MA0145.10.0144
MA0146.10.0539
MA0147.10.00212
MA0148.10.513
MA0149.10.00255
MA0150.10.00276
MA0152.10.718
MA0153.10.0217
MA0154.10.284
MA0155.10.108
MA0156.16.22135e-5
MA0157.10.0777
MA0159.10.0996
MA0160.10.0516
MA0162.10.18
MA0163.10.848
MA0164.10.772
MA0258.10.388
MA0259.10.00305



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: CNhs11846

Novel motifP-value
10.421
100.748
1000.148
1010.408
1020.671
1030.0573
1040.506
1050.336
1060.00199
1070.0211
1080.671
1090.248
110.992
1100.876
1110.508
1120.185
1130.697
1140.0459
1150.829
1160.567
1170.82
1180.721
1190.631
120.345
1200.691
1210.25
1220.635
1232.09199e-5
1240.0792
1250.981
1260.229
1270.213
1280.131
1290.737
130.926
1300.995
1310.462
1320.683
1330.719
1340.987
1350.0947
1360.382
1370.678
1380.696
1390.679
140.463
1400.949
1410.242
1420.738
1430.0537
1440.75
1450.451
1460.691
1470.978
1480.487
1490.13
150.832
1500.19
1510.269
1520.00136
1530.961
1540.168
1550.808
1560.867
1570.666
1580.4
1590.257
160.267
1600.731
1610.413
1620.762
1630.501
1640.414
1650.805
1660.827
1670.401
1680.199
1690.0365
170.461
180.36
190.13
20.0496
200.492
210.623
220.0328
230.0337
240.448
250.8
260.915
270.106
280.668
290.732
30.984
300.0531
310.259
320.0391
330.251
340.102
350.48
360.26
370.147
380.762
390.416
40.841
400.714
410.0652
420.437
430.274
440.666
450.243
460.605
470.702
480.993
490.986
50.39
500.425
510.497
520.114
530.269
540.367
550.29
560.794
570.167
580.968
590.0282
60.171
600.0506
610.707
620.588
630.967
640.602
650.666
660.652
670.757
680.597
690.738
70.921
700.371
710.754
720.155
730.00302
740.934
750.912
760.52
770.0715
780.798
790.103
80.955
800.0143
810.619
820.996
830.948
840.631
850.0454
860.615
870.202
880.498
890.0951
90.043
900.066
910.34
920.503
930.757
940.714
950.197
960.786
970.478
980.581
990.613



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: CNhs11846


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

DOID: Disease
0050686 (organ system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
3119 (gastrointestinal system cancer)
4 (disease)

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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