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{{f5samples
{{f5samples
|F5samples=
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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 16:56, 29 March 2012


Name:bronchioalveolar carcinoma cell line:NCI-H358
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
ageNA
cell typeclara cell
cell lineNCI-H358
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-penis0.321
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-lymphoma0.38
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11840

Jaspar motifP-value
MA0002.20.0794
MA0003.10.55
MA0004.10.936
MA0006.10.745
MA0007.10.867
MA0009.10.713
MA0014.10.0378
MA0017.10.55
MA0018.20.88
MA0019.10.76
MA0024.17.0464e-6
MA0025.10.825
MA0027.10.578
MA0028.17.24845e-4
MA0029.10.23
MA0030.10.265
MA0031.10.00397
MA0035.20.808
MA0038.10.00157
MA0039.21.92037e-4
MA0040.10.267
MA0041.10.62
MA0042.10.385
MA0043.10.308
MA0046.10.892
MA0047.20.0179
MA0048.10.809
MA0050.10.523
MA0051.10.269
MA0052.10.68
MA0055.10.00513
MA0057.10.67
MA0058.10.599
MA0059.10.987
MA0060.11.49316e-25
MA0061.10.00142
MA0062.20.0055
MA0065.20.0651
MA0066.10.331
MA0067.10.208
MA0068.10.00108
MA0069.10.48
MA0070.10.952
MA0071.10.418
MA0072.10.241
MA0073.10.831
MA0074.10.789
MA0076.10.00149
MA0077.10.354
MA0078.10.623
MA0079.20.442
MA0080.27.86247e-5
MA0081.10.0151
MA0083.10.238
MA0084.10.719
MA0087.10.669
MA0088.10.882
MA0090.10.989
MA0091.18.29043e-4
MA0092.10.0806
MA0093.10.847
MA0099.20.00216
MA0100.10.431
MA0101.10.0109
MA0102.20.739
MA0103.13.15677e-8
MA0104.20.0824
MA0105.15.56446e-4
MA0106.10.27
MA0107.10.00109
MA0108.20.78
MA0111.10.842
MA0112.20.639
MA0113.10.0238
MA0114.10.22
MA0115.10.335
MA0116.10.4
MA0117.10.0891
MA0119.10.112
MA0122.10.943
MA0124.10.471
MA0125.10.304
MA0131.10.819
MA0135.10.085
MA0136.10.0509
MA0137.20.434
MA0138.20.273
MA0139.10.015
MA0140.10.195
MA0141.10.2
MA0142.10.941
MA0143.10.99
MA0144.10.968
MA0145.10.42
MA0146.10.0308
MA0147.10.0526
MA0148.10.00528
MA0149.10.186
MA0150.10.92
MA0152.10.607
MA0153.10.764
MA0154.10.0016
MA0155.10.163
MA0156.10.455
MA0157.10.00574
MA0159.10.0592
MA0160.10.329
MA0162.10.823
MA0163.10.0918
MA0164.10.712
MA0258.10.697
MA0259.10.149



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: CNhs11840

Novel motifP-value
10.699
100.446
1000.201
1010.841
1020.229
1030.999
1040.799
1050.67
1060.118
1070.454
1080.368
1090.264
110.56
1100.91
1110.497
1120.011
1130.511
1140.501
1150.752
1160.248
1170.186
1180.557
1190.826
120.479
1200.435
1210.926
1220.383
1230.246
1240.215
1250.753
1260.226
1270.765
1280.0945
1290.88
130.0427
1300.422
1310.248
1320.629
1330.0106
1340.171
1350.0185
1360.0723
1370.0469
1380.216
1390.382
140.297
1400.18
1410.985
1420.789
1430.831
1440.285
1450.377
1460.641
1470.64
1480.232
1490.447
150.795
1500.854
1510.89
1520.545
1530.104
1540.708
1550.261
1560.522
1570.769
1580.543
1590.576
160.633
1600.593
1610.445
1620.373
1630.889
1640.00447
1650.997
1660.274
1670.328
1680.127
1690.497
170.853
180.0183
190.108
20.752
200.292
210.781
220.742
230.00258
240.742
250.741
260.274
270.432
280.549
290.702
30.683
300.671
310.137
320.00159
330.104
340.029
350.0401
360.699
370.788
380.843
390.663
40.0412
400.0664
410.327
420.764
430.184
440.516
450.524
460.899
470.882
480.978
490.975
50.463
500.746
510.704
520.554
530.877
540.801
550.825
560.967
570.829
580.469
590.317
60.556
600.515
610.244
620.118
630.957
640.848
650.566
662.55021e-8
670.945
680.012
690.288
70.709
700.877
710.436
720.411
730.599
740.0389
750.353
760.712
770.147
780.181
790.0902
80.856
800.0683
810.0321
820.182
830.877
840.811
850.0128
860.677
870.0542
880.896
890.999
90.0328
900.531
910.156
920.316
930.467
940.283
950.263
960.356
970.698
980.408
990.93



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: CNhs11840


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
0050615 (respiratory system cancer)
0050686 (organ system cancer)
0050687 (cell type cancer)
1324 (lung cancer)
1325 (bronchus cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
3904 (bronchogenic carcinoma)
3905 (lung carcinoma)
3908 (non-small cell lung carcinoma)
3910 (lung adenocarcinoma)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000025 (tube)
0000058 (duct)
0000060 (anatomical wall)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000115 (lung epithelium)
0000117 (respiratory tube)
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)
0000487 (simple squamous epithelium)
0000490 (unilaminar 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)
0001558 (lower respiratory tract)
0002048 (lung)
0002050 (embryonic structure)
0002169 (alveolar sac)
0002173 (alveolar duct)
0002186 (bronchiole)
0002224 (thoracic cavity)
0002299 (alveolus of lung)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003215 (alveolus)
0003258 (endoderm of foregut)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004802 (respiratory tract epithelium)
0004807 (respiratory system epithelium)
0004821 (pulmonary alveolus epithelium)
0004894 (alveolar wall)
0004903 (bronchoalveolar duct junction)
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)
0006524 (alveolar system)
0006914 (squamous epithelium)
0007026 (primitive gut)
0007196 (tracheobronchial tree)
0007499 (epithelial sac)
0008874 (pulmonary acinus)
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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