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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: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
|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: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
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|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 16:42, 29 March 2012


Name:lung adenocarcinoma cell line:A549
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 typepneumocyte, type ii, great alveolar cell (septal cell)
cell lineA549
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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
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-lymphoma0.0598
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: CNhs11275

Jaspar motifP-value
MA0002.20.0243
MA0003.10.45
MA0004.10.00922
MA0006.10.614
MA0007.10.869
MA0009.10.167
MA0014.13.31125e-4
MA0017.10.0034
MA0018.20.769
MA0019.10.0255
MA0024.10.659
MA0025.10.461
MA0027.10.52
MA0028.11.01919e-5
MA0029.10.744
MA0030.10.0356
MA0031.10.0639
MA0035.20.223
MA0038.10.85
MA0039.20.0012
MA0040.10.939
MA0041.10.943
MA0042.10.963
MA0043.10.0523
MA0046.13.02532e-45
MA0047.28.12078e-6
MA0048.10.41
MA0050.12.36198e-4
MA0051.10.024
MA0052.16.57912e-4
MA0055.12.61641e-4
MA0057.10.564
MA0058.10.00104
MA0059.10.0968
MA0060.10.668
MA0061.10.00916
MA0062.29.26424e-5
MA0065.20.177
MA0066.10.257
MA0067.10.658
MA0068.10.47
MA0069.10.458
MA0070.10.459
MA0071.10.836
MA0072.10.619
MA0073.10.819
MA0074.10.685
MA0076.11.00136e-5
MA0077.10.819
MA0078.10.565
MA0079.20.447
MA0080.28.50301e-7
MA0081.10.0289
MA0083.10.00752
MA0084.10.282
MA0087.10.198
MA0088.10.366
MA0090.10.15
MA0091.10.0187
MA0092.10.188
MA0093.10.00125
MA0099.24.25947e-4
MA0100.10.457
MA0101.10.506
MA0102.20.0362
MA0103.12.19882e-4
MA0104.20.0118
MA0105.12.12018e-4
MA0106.10.143
MA0107.10.101
MA0108.22.31879e-5
MA0111.10.775
MA0112.20.606
MA0113.10.0932
MA0114.17.84754e-6
MA0115.10.0353
MA0116.10.00908
MA0117.10.55
MA0119.10.361
MA0122.10.561
MA0124.10.221
MA0125.10.983
MA0131.10.215
MA0135.10.679
MA0136.13.60703e-4
MA0137.20.533
MA0138.20.0616
MA0139.19.35165e-5
MA0140.10.756
MA0141.10.218
MA0142.10.298
MA0143.10.447
MA0144.10.697
MA0145.10.751
MA0146.10.539
MA0147.10.0165
MA0148.12.27546e-4
MA0149.10.415
MA0150.16.11058e-4
MA0152.10.86
MA0153.14.66797e-42
MA0154.10.00847
MA0155.10.0904
MA0156.10.194
MA0157.10.975
MA0159.10.704
MA0160.10.125
MA0162.10.883
MA0163.10.0024
MA0164.10.332
MA0258.10.382
MA0259.10.164



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: CNhs11275

Novel motifP-value
10.874
100.804
1000.02
1010.214
1020.181
1030.152
1040.785
1050.238
1060.024
1070.18
1080.982
1090.843
110.569
1100.711
1110.994
1120.168
1130.104
1140.864
1150.927
1160.678
1170.932
1180.917
1190.571
120.891
1200.294
1210.0132
1220.709
1230.205
1240.849
1250.18
1260.96
1270.162
1280.00318
1290.475
130.298
1300.853
1310.701
1320.436
1330.525
1340.908
1350.325
1360.174
1370.324
1380.584
1390.939
140.758
1400.732
1410.564
1420.628
1430.0196
1440.45
1450.0312
1460.709
1470.825
1480.847
1490.551
150.748
1500.232
1510.135
1520.803
1530.861
1540.966
1550.356
1560.778
1570.374
1580.0725
1590.0712
160.381
1600.11
1610.33
1620.167
1630.382
1640.405
1650.969
1660.86
1670.957
1680.406
1690.508
170.338
180.251
190.186
20.455
200.0434
210.893
220.0608
230.105
240.996
250.544
260.404
270.162
280.53
290.972
30.625
300.879
310.417
329.57509e-4
330.761
340.408
350.127
360.664
370.887
380.387
390.807
40.949
400.591
410.0193
420.605
430.0453
440.174
450.866
460.281
470.824
480.814
490.0587
50.643
500.47
510.314
520.594
530.812
540.755
550.761
560.825
570.947
580.598
590.087
60.679
600.233
610.0561
620.0725
630.858
640.523
650.0569
660.454
670.395
680.153
690.725
70.634
700.199
710.513
720.419
730.753
740.356
750.43
760.523
770.922
780.414
790.0692
80.436
800.437
810.475
820.044
830.542
840.407
850.393
860.807
870.034
880.721
890.0543
90.0258
900.474
910.0244
920.205
930.647
940.126
950.59
960.463
970.665
980.186
990.16



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: CNhs11275


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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