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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 16:43, 29 March 2012


Name:large cell lung carcinoma cell line:IA-LM
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
age68
cell typeunclassifiable
cell lineIA-LM
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-penis-0.0693
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-0.185
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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: CNhs11277

Jaspar motifP-value
MA0002.20.456
MA0003.10.286
MA0004.10.758
MA0006.10.212
MA0007.10.64
MA0009.10.582
MA0014.10.797
MA0017.10.25
MA0018.20.149
MA0019.10.396
MA0024.10.0417
MA0025.10.134
MA0027.10.404
MA0028.11.07156e-4
MA0029.10.177
MA0030.10.118
MA0031.19.42722e-4
MA0035.20.296
MA0038.10.415
MA0039.20.693
MA0040.10.678
MA0041.10.76
MA0042.10.587
MA0043.10.853
MA0046.10.46
MA0047.20.046
MA0048.10.0519
MA0050.10.213
MA0051.15.6859e-4
MA0052.10.0663
MA0055.10.00185
MA0057.10.554
MA0058.10.67
MA0059.10.222
MA0060.10.82
MA0061.10.683
MA0062.25.65764e-4
MA0065.20.206
MA0066.10.756
MA0067.10.24
MA0068.10.00197
MA0069.10.631
MA0070.10.704
MA0071.10.609
MA0072.10.249
MA0073.10.498
MA0074.10.158
MA0076.13.84067e-4
MA0077.10.488
MA0078.10.706
MA0079.20.49
MA0080.27.56559e-6
MA0081.10.694
MA0083.10.918
MA0084.10.427
MA0087.10.747
MA0088.10.00163
MA0090.10.375
MA0091.10.0207
MA0092.10.332
MA0093.10.917
MA0099.21.61703e-16
MA0100.10.68
MA0101.10.222
MA0102.20.223
MA0103.10.0494
MA0104.20.0352
MA0105.10.143
MA0106.10.552
MA0107.10.603
MA0108.25.23616e-4
MA0111.10.555
MA0112.20.079
MA0113.10.241
MA0114.10.551
MA0115.10.961
MA0116.10.794
MA0117.10.893
MA0119.10.779
MA0122.10.877
MA0124.10.466
MA0125.10.34
MA0131.10.584
MA0135.10.0298
MA0136.10.0627
MA0137.20.0109
MA0138.20.363
MA0139.10.071
MA0140.10.0355
MA0141.10.0772
MA0142.10.0638
MA0143.10.813
MA0144.10.398
MA0145.10.1
MA0146.10.621
MA0147.10.0074
MA0148.10.00769
MA0149.10.404
MA0150.10.00642
MA0152.10.957
MA0153.10.202
MA0154.10.59
MA0155.10.44
MA0156.10.583
MA0157.19.75701e-4
MA0159.10.639
MA0160.10.477
MA0162.10.691
MA0163.10.097
MA0164.10.196
MA0258.10.343
MA0259.10.0479



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: CNhs11277

Novel motifP-value
10.784
100.385
1000.789
1010.372
1020.657
1030.305
1040.685
1050.709
1060.388
1070.795
1080.394
1090.894
110.504
1100.578
1110.0633
1120.0793
1130.704
1140.862
1150.0523
1160.17
1170.00673
1180.767
1190.533
120.474
1200.0892
1210.927
1220.656
1230.373
1240.854
1250.582
1260.925
1270.976
1280.143
1290.972
130.267
1300.371
1310.842
1320.879
1330.1
1340.586
1350.0331
1360.211
1370.931
1380.486
1390.949
140.379
1400.264
1410.66
1420.18
1430.764
1440.696
1450.15
1460.159
1470.932
1480.0469
1490.126
150.851
1500.825
1510.352
1520.971
1530.28
1540.857
1550.531
1560.727
1570.676
1580.335
1590.0564
160.258
1600.481
1610.925
1620.988
1630.0339
1640.933
1650.728
1660.306
1670.641
1680.625
1690.41
170.625
180.908
190.022
20.0148
201.79696e-4
210.688
220.298
230.00545
240.358
250.229
260.795
270.0507
280.128
290.117
30.563
300.407
310.474
328.76076e-4
330.744
340.196
350.167
360.15
370.643
380.568
390.343
40.0536
400.675
410.202
420.111
430.827
440.0852
450.254
460.915
470.726
480.938
490.438
50.737
500.481
510.104
520.183
530.867
540.295
550.58
560.914
570.381
580.913
590.477
60.931
600.159
610.0528
620.489
630.817
640.306
650.00621
662.77038e-6
670.263
680.996
690.862
70.913
700.337
710.785
720.526
730.748
740.644
750.0161
760.00274
770.161
780.609
790.249
80.194
800.408
810.619
820.202
830.115
840.386
850.361
860.44
870.241
880.822
890.0339
90.275
900.799
910.0588
920.777
930.793
940.628
950.441
960.38
970.546
980.708
990.859



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: CNhs11277


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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