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FF:10844-111E7: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120
|fonse_cell_line=FF:0101120
|fonse_cell_line_closure=FF:0101120
|fonse_cell_line_closure=FF:0101120

Revision as of 17:25, 29 March 2012


Name:merkel cell carcinoma cell line:MS-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
dev stageNA
sexunknown
ageunknown
cell typemerkel cell
cell lineMS-1
companyECACC
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-Neural0.0588
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-penis0.0732
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-lymphoma0.538
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: CNhs12839

Jaspar motifP-value
MA0002.21.57561e-6
MA0003.10.208
MA0004.10.507
MA0006.10.201
MA0007.10.298
MA0009.10.211
MA0014.10.984
MA0017.10.00422
MA0018.29.33916e-4
MA0019.10.796
MA0024.14.91116e-7
MA0025.10.201
MA0027.10.511
MA0028.10.131
MA0029.10.655
MA0030.10.26
MA0031.10.912
MA0035.20.435
MA0038.10.0105
MA0039.20.617
MA0040.10.859
MA0041.10.319
MA0042.10.24
MA0043.10.144
MA0046.10.711
MA0047.20.218
MA0048.10.392
MA0050.14.82299e-12
MA0051.12.14574e-5
MA0052.10.179
MA0055.10.909
MA0057.10.163
MA0058.10.482
MA0059.10.58
MA0060.12.04764e-21
MA0061.10.00349
MA0062.20.0444
MA0065.20.00412
MA0066.10.0929
MA0067.10.6
MA0068.10.0612
MA0069.10.0921
MA0070.17.85497e-4
MA0071.10.341
MA0072.10.699
MA0073.10.593
MA0074.10.16
MA0076.10.0126
MA0077.12.25282e-4
MA0078.10.481
MA0079.20.85
MA0080.23.96338e-11
MA0081.10.0388
MA0083.15.09838e-4
MA0084.10.594
MA0087.10.822
MA0088.10.768
MA0090.10.00124
MA0091.10.436
MA0092.10.24
MA0093.10.408
MA0099.23.13198e-14
MA0100.10.264
MA0101.10.0083
MA0102.20.0395
MA0103.10.061
MA0104.20.0897
MA0105.10.00286
MA0106.10.278
MA0107.10.0029
MA0108.20.934
MA0111.10.528
MA0112.21.13425e-4
MA0113.10.00569
MA0114.10.0268
MA0115.10.86
MA0116.10.0139
MA0117.10.953
MA0119.10.188
MA0122.10.428
MA0124.10.556
MA0125.10.0159
MA0131.10.519
MA0135.10.249
MA0136.17.06913e-7
MA0137.20.0242
MA0138.20.311
MA0139.10.324
MA0140.10.0855
MA0141.10.0331
MA0142.10.36
MA0143.10.819
MA0144.10.0119
MA0145.10.0938
MA0146.10.0934
MA0147.10.185
MA0148.10.228
MA0149.10.0115
MA0150.11.90783e-4
MA0152.10.648
MA0153.10.105
MA0154.10.05
MA0155.10.345
MA0156.10.013
MA0157.10.539
MA0159.10.0188
MA0160.10.0464
MA0162.10.215
MA0163.16.39084e-4
MA0164.10.631
MA0258.10.0194
MA0259.10.285



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: CNhs12839

Novel motifP-value
10.0853
100.125
1000.704
1010.268
1020.583
1030.086
1040.532
1050.54
1060.00178
1070.0433
1080.657
1090.0337
110.0651
1100.382
1110.157
1120.124
1130.708
1140.0162
1150.531
1160.416
1170.197
1180.37
1190.269
120.856
1200.778
1210.655
1220.495
1230.713
1240.448
1250.913
1260.187
1270.198
1280.0144
1290.334
130.197
1300.569
1310.174
1320.811
1330.606
1340.792
1350.07
1360.899
1370.31
1380.212
1390.126
140.662
1400.272
1410.692
1420.276
1430.0142
1440.577
1450.117
1460.966
1470.788
1480.0545
1490.0184
150.167
1500.626
1510.333
1520.0166
1530.206
1540.797
1550.913
1560.984
1570.35
1580.813
1590.834
160.104
1600.379
1610.493
1620.885
1630.238
1640.123
1650.0855
1660.622
1670.352
1680.0499
1690.00953
170.21
180.227
190.0506
20.412
200.906
210.0928
220.0882
230.00635
240.293
250.868
260.244
270.489
280.888
290.452
30.0308
300.747
310.375
320.00255
330.412
340.408
350.641
360.652
370.0472
380.44
390.244
40.717
400.48
410.331
420.257
430.106
440.332
450.382
460.238
470.363
480.269
490.194
50.0978
500.216
510.4
520.156
530.448
540.173
550.0194
560.559
570.548
580.345
590.0663
60.439
600.013
610.366
620.114
630.0812
640.753
650.173
660.466
670.934
680.819
690.873
70.391
700.0286
710.075
720.25
730.0134
740.247
750.0808
760.577
770.109
780.263
790.0522
80.167
800.064
810.256
820.0853
830.547
840.552
850.00701
860.291
870.429
880.873
890.0679
90.339
900.0717
910.126
920.0444
930.918
940.0924
950.131
960.162
970.87
980.222
990.646



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: CNhs12839


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)
0000034 (stem cell)
0000035 (single fate stem cell)
0000036 (epithelial fate stem cell)
0000066 (epithelial cell)
0000076 (squamous epithelial cell)
0000079 (stratified epithelial cell)
0000095 (neuron associated cell)
0000114 (surface ectodermal cell)
0000123 (neuron associated cell (sensu Vertebrata))
0000133 (neurectodermal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000237 (keratinizing barrier epithelial cell)
0000240 (stratified squamous epithelial cell)
0000242 (Merkel cell)
0000255 (eukaryotic cell)
0000311 (keratin accumulating cell)
0000312 (keratinocyte)
0000325 (stuff accumulating cell)
0000333 (migratory neural crest cell)
0000357 (stratified epithelial stem cell)
0000362 (epidermal cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002077 (ecto-epithelial cell)
0002159 (general ecto-epithelial cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001003 (skin epidermis)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002097 (skin of body)
0002199 (integument)
0002416 (integumental system)
0002532 (epiblast (generic))
0003102 (surface structure)
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)
0007376 (outer epithelium)
0007383 (enveloping layer of ectoderm)

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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