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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 16:56, 29 March 2012


Name:bronchogenic carcinoma cell line:ChaGo-K-1
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
age45
cell typeunclassifiable
cell lineChaGo-K-1
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-penis0.502
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-lymphoma0.501
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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: CNhs11841

Jaspar motifP-value
MA0002.21.25231e-4
MA0003.10.522
MA0004.10.276
MA0006.10.503
MA0007.10.404
MA0009.10.256
MA0014.10.167
MA0017.10.792
MA0018.20.00891
MA0019.10.481
MA0024.12.24336e-4
MA0025.10.828
MA0027.10.675
MA0028.10.0037
MA0029.10.577
MA0030.10.362
MA0031.10.304
MA0035.20.661
MA0038.10.0407
MA0039.20.00137
MA0040.10.523
MA0041.10.12
MA0042.10.424
MA0043.10.657
MA0046.10.843
MA0047.20.328
MA0048.10.345
MA0050.10.0459
MA0051.10.228
MA0052.11.36618e-4
MA0055.10.00257
MA0057.10.515
MA0058.10.201
MA0059.10.281
MA0060.11.2199e-5
MA0061.13.09524e-5
MA0062.20.0133
MA0065.20.0706
MA0066.10.235
MA0067.10.888
MA0068.10.104
MA0069.10.597
MA0070.10.499
MA0071.10.72
MA0072.10.789
MA0073.10.564
MA0074.10.827
MA0076.10.00722
MA0077.10.962
MA0078.10.131
MA0079.20.19
MA0080.21.0727e-7
MA0081.10.0587
MA0083.12.98929e-4
MA0084.10.0632
MA0087.10.3
MA0088.10.443
MA0090.10.809
MA0091.10.00241
MA0092.10.359
MA0093.10.242
MA0099.21.70506e-6
MA0100.10.273
MA0101.10.0058
MA0102.20.0285
MA0103.11.19171e-6
MA0104.20.191
MA0105.19.24466e-7
MA0106.10.186
MA0107.11.64206e-4
MA0108.20.0492
MA0111.10.761
MA0112.20.385
MA0113.10.138
MA0114.10.142
MA0115.10.0872
MA0116.10.0114
MA0117.10.63
MA0119.10.155
MA0122.10.655
MA0124.10.945
MA0125.10.427
MA0131.10.24
MA0135.10.901
MA0136.14.12711e-5
MA0137.20.609
MA0138.20.109
MA0139.10.562
MA0140.10.331
MA0141.10.608
MA0142.10.0191
MA0143.10.72
MA0144.10.185
MA0145.10.988
MA0146.10.0543
MA0147.10.159
MA0148.10.903
MA0149.10.065
MA0150.10.448
MA0152.10.369
MA0153.10.49
MA0154.10.00174
MA0155.10.102
MA0156.10.133
MA0157.10.112
MA0159.10.353
MA0160.10.79
MA0162.10.761
MA0163.10.0097
MA0164.10.127
MA0258.10.329
MA0259.10.39



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: CNhs11841

Novel motifP-value
10.992
100.757
1000.609
1010.583
1020.414
1030.224
1040.158
1050.257
1060.0151
1070.124
1080.816
1090.072
110.242
1100.935
1110.653
1120.0238
1130.0375
1140.325
1150.195
1160.868
1170.181
1180.747
1190.587
120.618
1200.573
1210.466
1220.129
1230.756
1240.636
1250.534
1260.471
1270.685
1280.169
1290.359
130.188
1300.513
1310.14
1320.395
1333.26225e-5
1340.129
1350.0206
1360.00762
1370.327
1380.831
1390.00386
140.661
1400.799
1410.532
1420.909
1430.0103
1440.517
1450.924
1460.434
1470.88
1480.346
1490.0729
150.729
1500.534
1510.873
1520.841
1530.456
1540.836
1550.213
1560.997
1570.445
1580.146
1590.251
160.923
1600.998
1610.527
1620.769
1630.785
1640.781
1650.282
1660.623
1670.102
1680.11
1690.863
170.691
180.0337
190.107
20.386
200.158
210.817
220.654
230.00255
240.686
250.499
260.946
270.201
280.627
290.261
30.305
300.946
310.283
320.0776
330.543
340.216
350.0733
360.603
370.702
380.967
390.523
40.932
400.715
410.0151
420.628
430.0875
440.669
450.453
460.135
470.958
480.776
490.24
50.267
500.779
510.719
520.713
530.612
540.52
550.172
560.361
570.967
580.914
590.118
60.464
600.19
610.415
620.405
630.809
640.81
650.169
660.0325
670.736
680.28
690.607
70.527
700.0652
710.918
720.614
730.842
740.0981
750.923
760.316
770.463
780.674
790.0181
80.933
800.00794
810.204
820.0428
830.0765
840.942
850.00107
860.282
870.122
880.364
890.124
90.0757
900.187
910.182
920.161
930.216
940.43
950.0304
960.246
970.353
980.809
990.889



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: CNhs11841


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)
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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