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FF:10846-111E9: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100353,FF:0101120,FF:0102424
|fonse_cell_line=FF:0100353,FF:0101120,FF:0102424
|fonse_cell_line_closure=FF:0100353,FF:0101120,FF:0102424
|fonse_cell_line_closure=FF:0100353,FF:0101120,FF:0102424

Revision as of 17:28, 29 March 2012


Name:mesothelioma cell line:NCI-H226
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuemesothelium
dev stageNA
sexmale
ageunknown
cell typemesothelial cell
cell lineNCI-H226
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-penis0.222
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-lymphoma0.421
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs13062

Jaspar motifP-value
MA0002.20.0714
MA0003.10.343
MA0004.10.798
MA0006.10.0844
MA0007.10.884
MA0009.10.94
MA0014.10.949
MA0017.10.857
MA0018.21.52024e-4
MA0019.10.252
MA0024.10.0384
MA0025.10.294
MA0027.10.852
MA0028.17.1718e-4
MA0029.10.111
MA0030.10.00415
MA0031.18.16404e-5
MA0035.20.0176
MA0038.10.565
MA0039.20.539
MA0040.10.196
MA0041.10.0667
MA0042.10.0617
MA0043.10.0132
MA0046.10.0379
MA0047.21.73417e-4
MA0048.10.00181
MA0050.10.159
MA0051.10.901
MA0052.14.65769e-4
MA0055.19.27713e-4
MA0057.10.357
MA0058.10.924
MA0059.10.166
MA0060.10.778
MA0061.10.964
MA0062.20.0837
MA0065.20.0849
MA0066.10.709
MA0067.10.00197
MA0068.10.17
MA0069.10.08
MA0070.10.923
MA0071.10.541
MA0072.10.277
MA0073.10.649
MA0074.10.7
MA0076.10.103
MA0077.10.466
MA0078.10.176
MA0079.20.17
MA0080.22.96127e-8
MA0081.10.085
MA0083.10.0168
MA0084.10.368
MA0087.10.184
MA0088.10.0363
MA0090.15.97981e-6
MA0091.10.162
MA0092.10.429
MA0093.10.716
MA0099.21.11382e-4
MA0100.10.818
MA0101.10.821
MA0102.20.109
MA0103.10.0355
MA0104.20.364
MA0105.10.964
MA0106.10.00109
MA0107.10.993
MA0108.20.383
MA0111.10.112
MA0112.20.163
MA0113.10.714
MA0114.10.094
MA0115.10.242
MA0116.10.834
MA0117.10.364
MA0119.10.052
MA0122.10.897
MA0124.10.088
MA0125.10.299
MA0131.10.62
MA0135.10.0823
MA0136.16.14772e-6
MA0137.20.267
MA0138.20.0019
MA0139.10.559
MA0140.10.0292
MA0141.10.944
MA0142.10.808
MA0143.10.373
MA0144.10.15
MA0145.10.482
MA0146.10.0688
MA0147.10.0721
MA0148.10.0176
MA0149.10.213
MA0150.10.886
MA0152.10.722
MA0153.10.046
MA0154.10.298
MA0155.10.938
MA0156.10.155
MA0157.10.0152
MA0159.10.0267
MA0160.10.515
MA0162.10.119
MA0163.10.752
MA0164.10.274
MA0258.10.439
MA0259.10.77



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: CNhs13062

Novel motifP-value
10.568
100.541
1000.065
1010.778
1020.803
1030.163
1040.909
1050.364
1060.176
1070.12
1080.893
1090.0358
110.516
1100.047
1110.778
1120.783
1130.0108
1140.248
1150.864
1160.0989
1170.257
1180.227
1190.821
120.813
1200.286
1210.936
1220.593
1230.94
1240.0932
1250.823
1260.962
1270.937
1280.789
1290.734
130.0191
1300.968
1310.88
1320.584
1330.0822
1340.0857
1350.00346
1360.0135
1370.0772
1380.737
1390.144
140.352
1400.297
1410.492
1420.614
1430.205
1440.902
1450.729
1460.426
1470.735
1480.641
1490.346
150.943
1500.0999
1510.944
1520.0333
1530.258
1540.831
1550.715
1560.858
1570.379
1580.0128
1590.467
160.283
1600.227
1610.154
1620.577
1630.945
1640.0591
1650.286
1660.82
1670.936
1680.313
1690.0224
170.959
180.904
190.855
20.889
200.244
210.00383
220.819
230.0361
240.187
250.345
260.481
270.9
280.157
290.26
30.655
300.552
310.497
320.389
330.459
340.746
350.705
360.667
370.17
380.841
390.349
40.535
400.515
410.0091
420.666
430.0924
440.48
450.975
460.83
470.489
480.224
490.16
50.0832
500.467
510.518
520.596
530.882
540.399
550.614
560.476
570.0838
580.287
590.488
60.833
600.991
610.443
620.37
630.279
640.804
650.553
660.0306
670.717
680.849
690.109
70.793
700.951
710.0901
720.202
730.143
740.834
750.526
760.174
770.0555
780.154
790.568
80.249
800.0786
810.375
820.717
830.759
840.986
850.0459
860.583
870.0108
880.268
890.275
90.225
900.227
910.187
920.0489
930.697
940.494
950.132
960.583
970.823
980.653
990.379



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: CNhs13062


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)
0000076 (squamous epithelial cell)
0000077 (mesothelial cell)
0000213 (lining cell)
0000215 (barrier cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002321 (embryonic 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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