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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000118,UBERON:0000119,UBERON:0000170,UBERON:0000171,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002048,UBERON:0002050,UBERON:0002224,UBERON:0002384,UBERON:0002532,UBERON:0003104,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005597,UBERON:0005911,UBERON:0007026,UBERON:0008947,UBERON:0009142
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000066,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000066,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100353,FF:0100400,FF:0100453,FF:0101120
|fonse_cell_line=FF:0100353,FF:0100400,FF:0100453,FF:0101120
|fonse_cell_line_closure=FF:0100353,FF:0100400,FF:0100453,FF:0101120
|fonse_cell_line_closure=FF:0100353,FF:0100400,FF:0100453,FF:0101120

Revision as of 17:13, 29 March 2012


Name:non-small cell lung cancer cell line:NCI-H1385
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
sexfemale
age49
cell typeneuroendocrine cell
cell lineNCI-H1385
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-penis-0.0407
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
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: CNhs12193

Jaspar motifP-value
MA0002.20.00522
MA0003.10.319
MA0004.10.917
MA0006.10.22
MA0007.10.124
MA0009.10.578
MA0014.10.597
MA0017.10.0519
MA0018.21.74867e-5
MA0019.10.877
MA0024.18.52742e-5
MA0025.10.00204
MA0027.10.84
MA0028.10.00749
MA0029.10.396
MA0030.10.111
MA0031.10.477
MA0035.20.26
MA0038.12.38732e-6
MA0039.20.341
MA0040.10.744
MA0041.10.34
MA0042.10.871
MA0043.10.00719
MA0046.10.405
MA0047.20.0128
MA0048.10.0585
MA0050.17.86532e-17
MA0051.13.54612e-8
MA0052.10.231
MA0055.10.295
MA0057.10.243
MA0058.10.553
MA0059.10.551
MA0060.14.17969e-20
MA0061.10.00649
MA0062.20.00359
MA0065.20.0162
MA0066.10.169
MA0067.10.625
MA0068.10.888
MA0069.10.545
MA0070.10.0172
MA0071.10.826
MA0072.10.188
MA0073.10.381
MA0074.10.131
MA0076.13.89119e-4
MA0077.10.232
MA0078.10.773
MA0079.20.742
MA0080.29.37168e-10
MA0081.10.268
MA0083.10.00315
MA0084.10.627
MA0087.10.566
MA0088.10.33
MA0090.10.00198
MA0091.10.162
MA0092.10.214
MA0093.10.65
MA0099.22.57262e-4
MA0100.10.128
MA0101.10.0115
MA0102.20.0311
MA0103.10.0072
MA0104.20.276
MA0105.10.00667
MA0106.10.309
MA0107.10.0116
MA0108.20.0481
MA0111.10.698
MA0112.20.00125
MA0113.10.143
MA0114.10.0977
MA0115.10.632
MA0116.10.00826
MA0117.10.306
MA0119.10.0399
MA0122.10.729
MA0124.10.473
MA0125.10.00544
MA0131.10.232
MA0135.10.707
MA0136.12.42471e-5
MA0137.20.852
MA0138.20.356
MA0139.10.867
MA0140.10.341
MA0141.10.673
MA0142.10.434
MA0143.10.72
MA0144.10.195
MA0145.10.202
MA0146.10.03
MA0147.10.448
MA0148.10.0631
MA0149.10.232
MA0150.10.777
MA0152.10.925
MA0153.10.52
MA0154.10.0249
MA0155.10.4
MA0156.10.0248
MA0157.10.979
MA0159.10.0472
MA0160.10.916
MA0162.10.0987
MA0163.16.38834e-5
MA0164.10.0851
MA0258.10.035
MA0259.10.284



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: CNhs12193

Novel motifP-value
10.237
100.154
1000.425
1010.491
1020.27
1030.444
1040.684
1050.518
1066.41911e-5
1070.0191
1080.614
1090.112
110.125
1100.215
1110.0317
1120.116
1130.64
1140.0219
1150.376
1160.16
1170.0579
1180.322
1190.169
120.962
1200.739
1210.994
1220.184
1230.15
1240.572
1250.9
1260.1
1270.567
1280.0344
1290.966
130.0391
1300.316
1310.775
1320.567
1330.199
1340.468
1350.724
1360.493
1370.0792
1380.486
1390.0146
140.611
1400.685
1410.98
1420.945
1430.429
1440.256
1450.0446
1460.773
1470.804
1480.00247
1490.0755
150.201
1500.24
1510.235
1520.0232
1530.223
1540.79
1550.893
1560.742
1570.79
1580.905
1590.294
160.143
1600.155
1610.595
1620.19
1630.695
1640.0737
1650.199
1660.469
1670.192
1680.106
1690.00308
170.219
180.32
190.0383
20.679
200.438
210.035
220.116
230.0315
240.485
250.945
260.0132
270.662
280.74
290.273
30.125
300.93
310.747
320.00325
330.428
340.232
350.544
360.703
370.159
380.383
390.0679
40.533
400.176
410.465
420.907
430.0623
440.678
450.654
460.297
470.637
480.296
490.203
50.318
500.0492
510.628
520.054
530.542
540.274
550.125
560.867
570.489
580.482
590.0435
60.736
600.00613
610.0482
620.227
630.0145
640.649
650.192
660.117
670.961
680.734
690.333
70.499
700.0589
710.107
720.206
730.0556
740.649
750.249
760.262
770.137
780.0365
790.0388
80.129
800.639
810.232
820.147
830.714
840.608
850.0772
860.417
870.777
880.724
890.699
90.291
900.138
910.157
920.313
930.161
940.355
950.996
960.954
970.679
980.799
990.712



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: CNhs12193


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)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000066 (epithelial cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050687 (cell type cancer)
1115 (sarcoma)
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)
0002384 (connective tissue)
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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