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{{f5samples
{{f5samples
|F5samples=
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|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000058,UBERON:0000060,UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000065,UBERON:0000072,UBERON:0000077,UBERON:0000115,UBERON:0000117,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:0000487,UBERON:0000490,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0001558,UBERON:0002048,UBERON:0002050,UBERON:0002169,UBERON:0002173,UBERON:0002186,UBERON:0002224,UBERON:0002299,UBERON:0002532,UBERON:0003104,UBERON:0003215,UBERON:0003258,UBERON:0003914,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004802,UBERON:0004807,UBERON:0004821,UBERON:0004894,UBERON:0004903,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005597,UBERON:0005911,UBERON:0006524,UBERON:0006914,UBERON:0007026,UBERON:0007196,UBERON:0007499,UBERON:0008874,UBERON:0008947,UBERON:0009142
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
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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 16:55, 29 March 2012


Name:alveolar cell carcinoma cell line:SW 1573
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
age44
cell typepneumocyte
cell lineSW 1573
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-penis0.255
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-lymphoma0.532
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: CNhs11838

Jaspar motifP-value
MA0002.20.0201
MA0003.10.0189
MA0004.10.655
MA0006.10.666
MA0007.10.368
MA0009.10.421
MA0014.10.486
MA0017.10.409
MA0018.20.186
MA0019.10.337
MA0024.12.35471e-6
MA0025.10.772
MA0027.10.807
MA0028.10.0706
MA0029.10.633
MA0030.10.197
MA0031.10.734
MA0035.20.473
MA0038.10.288
MA0039.20.905
MA0040.10.436
MA0041.10.361
MA0042.10.582
MA0043.10.0141
MA0046.10.0912
MA0047.20.918
MA0048.10.00642
MA0050.11.75509e-7
MA0051.11.07786e-5
MA0052.10.0351
MA0055.10.00354
MA0057.10.736
MA0058.10.826
MA0059.10.214
MA0060.10.00237
MA0061.10.0083
MA0062.20.32
MA0065.20.268
MA0066.10.356
MA0067.10.342
MA0068.10.604
MA0069.10.343
MA0070.10.681
MA0071.10.932
MA0072.10.0873
MA0073.10.592
MA0074.10.882
MA0076.10.669
MA0077.10.242
MA0078.10.201
MA0079.20.161
MA0080.29.12134e-11
MA0081.10.0332
MA0083.10.583
MA0084.10.451
MA0087.10.457
MA0088.10.198
MA0090.10.228
MA0091.10.093
MA0092.10.431
MA0093.10.594
MA0099.20.0317
MA0100.10.0076
MA0101.10.0413
MA0102.20.00174
MA0103.10.759
MA0104.20.102
MA0105.10.0211
MA0106.10.683
MA0107.10.00408
MA0108.21.64882e-4
MA0111.10.461
MA0112.20.177
MA0113.10.255
MA0114.10.602
MA0115.10.535
MA0116.10.0557
MA0117.10.634
MA0119.10.622
MA0122.10.186
MA0124.10.361
MA0125.10.997
MA0131.10.22
MA0135.10.312
MA0136.11.082e-8
MA0137.20.0391
MA0138.20.208
MA0139.10.326
MA0140.10.898
MA0141.10.776
MA0142.10.618
MA0143.10.383
MA0144.10.00641
MA0145.10.173
MA0146.10.379
MA0147.10.112
MA0148.10.768
MA0149.10.165
MA0150.10.214
MA0152.10.299
MA0153.10.433
MA0154.10.0222
MA0155.10.014
MA0156.18.38264e-7
MA0157.10.376
MA0159.10.529
MA0160.10.309
MA0162.10.155
MA0163.10.178
MA0164.10.569
MA0258.10.31
MA0259.10.271



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: CNhs11838

Novel motifP-value
10.702
100.943
1000.168
1010.529
1020.754
1030.779
1040.505
1050.832
1060.00262
1070.258
1080.546
1090.491
110.796
1100.82
1110.258
1120.331
1130.682
1140.628
1150.849
1160.967
1170.982
1180.519
1190.344
120.952
1200.0584
1210.787
1220.589
1230.148
1240.195
1250.223
1260.25
1270.708
1280.0288
1290.998
130.719
1300.917
1310.29
1320.322
1330.19
1340.968
1350.0139
1360.0808
1370.174
1380.539
1390.629
140.799
1400.663
1410.801
1420.56
1430.606
1440.949
1450.617
1460.131
1470.229
1480.886
1490.0649
150.352
1500.973
1510.811
1520.342
1530.106
1540.51
1550.664
1560.491
1570.624
1580.407
1590.307
160.858
1600.916
1610.274
1620.858
1630.115
1640.331
1650.995
1660.454
1670.0391
1680.0713
1690.932
170.88
180.256
190.691
20.432
200.0646
210.06
220.261
230.0603
240.515
250.733
260.148
270.28
280.682
290.609
30.662
300.222
310.207
320.0168
330.642
340.14
350.909
360.949
370.291
380.471
390.807
40.325
400.269
410.277
420.397
430.223
440.107
450.0153
460.821
470.619
480.717
490.363
50.0516
500.932
510.798
520.0285
530.844
540.92
550.903
560.858
570.13
580.226
590.432
60.221
600.0442
610.914
620.396
630.944
640.724
650.113
660.16
670.828
680.902
690.643
70.725
700.248
710.934
720.0027
730.478
740.409
750.663
760.915
770.119
780.437
790.2
80.172
800.525
810.605
820.352
830.805
840.152
850.0555
860.414
870.955
880.599
890.0595
90.217
900.267
910.034
920.249
930.362
940.245
950.873
960.984
970.447
980.755
990.24



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: CNhs11838


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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