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FF:10843-111E6: 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:MKL-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
sexmale
age26
cell typemerkel cell
cell lineMKL-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
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-penis0.362
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-lymphoma0.657
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12838

Jaspar motifP-value
MA0002.23.11563e-5
MA0003.10.21
MA0004.10.634
MA0006.10.153
MA0007.10.323
MA0009.10.671
MA0014.10.75
MA0017.10.00608
MA0018.20.13
MA0019.10.885
MA0024.14.66447e-13
MA0025.10.93
MA0027.10.828
MA0028.10.392
MA0029.10.788
MA0030.10.826
MA0031.10.231
MA0035.20.47
MA0038.10.151
MA0039.20.0485
MA0040.10.359
MA0041.10.241
MA0042.10.0895
MA0043.10.661
MA0046.10.0444
MA0047.20.0133
MA0048.10.743
MA0050.13.92007e-11
MA0051.11.50413e-6
MA0052.11.32402e-4
MA0055.10.657
MA0057.10.151
MA0058.10.816
MA0059.10.577
MA0060.11.10234e-17
MA0061.10.00211
MA0062.20.622
MA0065.20.245
MA0066.10.309
MA0067.10.866
MA0068.10.206
MA0069.10.544
MA0070.10.0101
MA0071.10.43
MA0072.10.877
MA0073.10.607
MA0074.10.29
MA0076.10.0776
MA0077.10.0102
MA0078.10.705
MA0079.20.694
MA0080.28.26096e-12
MA0081.10.0252
MA0083.11.47144e-7
MA0084.10.771
MA0087.10.684
MA0088.10.484
MA0090.18.91919e-4
MA0091.10.468
MA0092.10.23
MA0093.10.625
MA0099.21.04644e-21
MA0100.10.147
MA0101.10.00115
MA0102.22.82999e-5
MA0103.10.00994
MA0104.20.0635
MA0105.10.0382
MA0106.10.31
MA0107.12.72158e-4
MA0108.21.01355e-5
MA0111.10.881
MA0112.20.00161
MA0113.10.00263
MA0114.10.0731
MA0115.10.106
MA0116.10.157
MA0117.10.558
MA0119.10.503
MA0122.10.369
MA0124.10.536
MA0125.10.232
MA0131.10.566
MA0135.10.972
MA0136.12.98356e-10
MA0137.25.61913e-5
MA0138.20.0985
MA0139.10.402
MA0140.10.336
MA0141.10.203
MA0142.10.111
MA0143.10.932
MA0144.11.62374e-4
MA0145.10.0455
MA0146.10.185
MA0147.10.127
MA0148.10.0237
MA0149.10.175
MA0150.16.96985e-6
MA0152.10.985
MA0153.10.0571
MA0154.10.053
MA0155.10.28
MA0156.12.15869e-6
MA0157.10.297
MA0159.10.117
MA0160.10.18
MA0162.10.217
MA0163.10.206
MA0164.10.482
MA0258.10.109
MA0259.10.155



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: CNhs12838

Novel motifP-value
10.753
100.596
1000.704
1010.375
1020.63
1030.75
1040.662
1050.141
1064.82172e-4
1070.0119
1080.979
1090.0962
110.385
1100.809
1110.59
1120.157
1130.457
1140.0985
1150.118
1160.738
1170.765
1180.455
1190.346
120.543
1200.798
1210.466
1220.844
1230.156
1240.351
1250.144
1260.288
1270.199
1280.0277
1290.49
130.577
1300.993
1310.0848
1320.549
1330.06
1340.568
1350.00569
1360.597
1370.439
1380.228
1390.0351
140.304
1400.923
1410.753
1420.74
1430.147
1440.185
1450.308
1460.748
1470.704
1480.169
1490.0117
150.372
1500.545
1510.347
1520.0102
1530.104
1540.849
1550.473
1560.702
1570.668
1580.544
1590.328
160.261
1600.45
1610.978
1620.783
1630.275
1640.239
1650.49
1660.602
1670.326
1680.0729
1690.0248
170.305
180.281
190.0846
20.14
200.556
210.229
220.0605
230.00511
240.371
250.995
260.803
270.332
280.976
290.896
30.066
300.21
310.674
320.012
330.573
340.196
350.878
360.73
370.0605
380.739
390.257
40.304
400.188
410.213
420.185
430.168
440.83
450.23
460.751
470.904
480.716
490.419
50.087
500.148
510.419
520.162
530.362
540.133
550.108
560.49
570.837
580.345
590.0865
60.668
600.0155
610.58
620.205
630.16
640.847
650.207
660.119
670.747
680.886
690.455
70.408
700.26
710.313
720.221
730.0106
740.686
750.325
760.781
770.0634
780.943
790.206
80.552
800.0172
810.447
820.321
830.083
840.664
850.00732
860.384
870.785
880.839
890.0956
90.107
900.546
910.299
920.0987
930.239
940.301
950.223
960.204
970.917
980.905
990.619



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: CNhs12838


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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