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FF:10839-111E2: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100353,FF:0101120
|fonse_cell_line=FF:0100353,FF:0101120
|fonse_cell_line_closure=FF:0100353,FF:0101120
|fonse_cell_line_closure=FF:0100353,FF:0101120

Revision as of 17:24, 29 March 2012


Name:large cell lung carcinoma cell line:NCI-H460
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stageNA
sexmale
ageunknown
cell typeunclassifiable
cell lineNCI-H460
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-penis0.149
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-lymphoma-0.159
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12806

Jaspar motifP-value
MA0002.20.041
MA0003.10.696
MA0004.10.496
MA0006.10.267
MA0007.10.878
MA0009.10.664
MA0014.10.434
MA0017.10.669
MA0018.20.501
MA0019.10.115
MA0024.10.426
MA0025.10.313
MA0027.10.679
MA0028.16.52047e-5
MA0029.10.45
MA0030.10.153
MA0031.10.697
MA0035.20.386
MA0038.10.00382
MA0039.20.851
MA0040.10.305
MA0041.10.728
MA0042.10.741
MA0043.10.277
MA0046.10.365
MA0047.20.065
MA0048.10.0983
MA0050.10.00389
MA0051.10.108
MA0052.10.0102
MA0055.10.0141
MA0057.10.674
MA0058.10.572
MA0059.10.052
MA0060.13.91662e-7
MA0061.10.0266
MA0062.20.00194
MA0065.20.551
MA0066.10.563
MA0067.10.703
MA0068.10.00644
MA0069.10.498
MA0070.10.189
MA0071.10.0574
MA0072.10.408
MA0073.10.57
MA0074.10.249
MA0076.18.60347e-4
MA0077.10.148
MA0078.10.446
MA0079.20.13
MA0080.21.43862e-7
MA0081.10.0348
MA0083.10.0102
MA0084.10.936
MA0087.10.177
MA0088.10.7
MA0090.10.592
MA0091.10.0619
MA0092.10.428
MA0093.10.364
MA0099.20.73
MA0100.10.312
MA0101.10.0152
MA0102.20.713
MA0103.10.122
MA0104.20.00266
MA0105.10.0773
MA0106.10.645
MA0107.10.00591
MA0108.22.8978e-4
MA0111.10.913
MA0112.20.0661
MA0113.10.0781
MA0114.10.55
MA0115.10.958
MA0116.10.947
MA0117.10.414
MA0119.10.575
MA0122.10.298
MA0124.10.457
MA0125.10.141
MA0131.10.483
MA0135.10.236
MA0136.12.08701e-5
MA0137.20.117
MA0138.20.301
MA0139.10.246
MA0140.10.992
MA0141.10.0187
MA0142.10.95
MA0143.10.787
MA0144.10.425
MA0145.10.431
MA0146.10.787
MA0147.10.00108
MA0148.11.39424e-4
MA0149.10.0554
MA0150.10.00172
MA0152.10.0436
MA0153.10.333
MA0154.10.405
MA0155.10.0475
MA0156.10.266
MA0157.10.832
MA0159.10.441
MA0160.10.685
MA0162.10.695
MA0163.10.812
MA0164.10.994
MA0258.10.0735
MA0259.10.0589



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: CNhs12806

Novel motifP-value
10.417
100.235
1000.00284
1010.29
1020.295
1030.725
1040.825
1050.00874
1060.13
1070.54
1080.122
1090.0692
110.911
1100.752
1110.809
1120.662
1130.018
1140.609
1150.684
1160.248
1170.902
1180.0186
1190.636
120.39
1200.0173
1210.00755
1220.975
1230.831
1240.173
1250.785
1260.711
1270.932
1280.507
1290.735
130.302
1300.557
1310.466
1320.389
1330.37
1340.187
1350.27
1360.0544
1370.0685
1380.939
1390.308
140.356
1400.65
1410.249
1420.103
1430.114
1440.251
1450.0267
1460.864
1470.123
1480.168
1490.888
150.0414
1500.829
1510.244
1520.201
1530.927
1540.788
1550.418
1560.633
1570.668
1580.311
1590.152
160.886
1600.701
1610.448
1620.859
1630.94
1640.0348
1650.848
1660.711
1670.216
1680.64
1690.95
170.954
180.0503
190.456
20.116
200.115
210.994
220.441
230.0826
240.261
250.484
260.257
270.743
280.755
290.00138
30.759
300.133
310.668
320.0446
330.47
340.254
350.415
360.12
370.46
380.611
390.757
40.152
400.201
410.465
420.822
430.269
440.0323
450.27
460.669
470.885
480.783
490.081
50.468
500.824
510.703
520.216
530.0827
540.549
550.898
560.588
570.408
580.903
590.915
60.0327
600.201
610.385
620.959
630.731
640.989
650.34
660.349
670.484
680.624
690.585
70.646
700.654
710.45
720.175
730.921
740.458
750.212
760.0138
770.29
780.873
790.361
80.0662
800.0623
810.561
820.216
830.795
840.0773
850.559
860.967
870.277
880.663
890.89
90.0925
900.701
910.00446
920.842
930.414
940.698
950.00155
960.0666
970.767
980.213
990.733



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: CNhs12806


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

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

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000118 (lung bud)
0000119 (cell layer)
0000170 (pair of lungs)
0000171 (respiration organ)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002048 (lung)
0002050 (embryonic structure)
0002224 (thoracic cavity)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003258 (endoderm of foregut)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005423 (developing anatomical structure)
0005597 (lung primordium)
0005911 (endo-epithelium)
0007026 (primitive gut)
0008947 (respiratory primordium)
0009142 (entire embryonic mesenchyme)

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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