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FF:10851-111F5: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0102424
|fonse_cell_line=FF:0102424
|fonse_cell_line_closure=FF:0102424
|fonse_cell_line_closure=FF:0102424

Revision as of 17:28, 29 March 2012


Name:mesothelioma cell line:Mero-41
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
age60
cell typemesothelial cell
cell lineMero-41
companyECACC
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-penis0.0301
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-lymphoma0.413
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs13067

Jaspar motifP-value
MA0002.20.244
MA0003.10.324
MA0004.10.678
MA0006.10.318
MA0007.10.695
MA0009.10.76
MA0014.10.351
MA0017.10.697
MA0018.21.73242e-6
MA0019.10.891
MA0024.14.64257e-5
MA0025.10.00203
MA0027.10.598
MA0028.10.0436
MA0029.10.963
MA0030.10.0159
MA0031.10.00479
MA0035.20.573
MA0038.10.726
MA0039.20.79
MA0040.10.92
MA0041.10.86
MA0042.10.79
MA0043.11.66743e-9
MA0046.10.383
MA0047.20.0304
MA0048.10.0017
MA0050.10.314
MA0051.10.387
MA0052.10.00149
MA0055.10.00436
MA0057.10.144
MA0058.10.155
MA0059.10.0815
MA0060.10.258
MA0061.10.337
MA0062.20.586
MA0065.20.117
MA0066.10.375
MA0067.16.87172e-4
MA0068.18.43059e-5
MA0069.10.769
MA0070.10.605
MA0071.10.589
MA0072.10.132
MA0073.10.705
MA0074.10.759
MA0076.10.829
MA0077.10.368
MA0078.10.86
MA0079.20.0218
MA0080.22.94732e-12
MA0081.10.0044
MA0083.10.365
MA0084.10.414
MA0087.10.401
MA0088.10.00249
MA0090.10.00302
MA0091.10.964
MA0092.10.248
MA0093.10.799
MA0099.20.179
MA0100.10.731
MA0101.10.254
MA0102.25.50757e-4
MA0103.10.465
MA0104.20.343
MA0105.10.679
MA0106.10.0264
MA0107.10.109
MA0108.20.0169
MA0111.10.846
MA0112.20.00897
MA0113.10.515
MA0114.10.0866
MA0115.10.172
MA0116.10.959
MA0117.10.929
MA0119.10.00765
MA0122.10.514
MA0124.10.56
MA0125.10.749
MA0131.10.877
MA0135.10.00612
MA0136.12.01726e-9
MA0137.20.504
MA0138.20.0839
MA0139.10.683
MA0140.10.662
MA0141.10.532
MA0142.10.386
MA0143.10.976
MA0144.10.909
MA0145.10.212
MA0146.10.872
MA0147.10.135
MA0148.10.106
MA0149.10.0833
MA0150.10.155
MA0152.10.74
MA0153.10.251
MA0154.10.949
MA0155.10.931
MA0156.10.00178
MA0157.10.0324
MA0159.10.736
MA0160.10.886
MA0162.10.392
MA0163.10.311
MA0164.10.314
MA0258.10.348
MA0259.10.863



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: CNhs13067

Novel motifP-value
10.32
100.423
1000.14
1010.236
1020.314
1030.272
1040.752
1050.0248
1060.577
1070.0454
1080.887
1090.0826
110.793
1100.546
1110.994
1120.762
1130.00921
1140.402
1150.309
1160.453
1170.891
1180.488
1190.301
120.774
1200.276
1210.663
1220.422
1230.0839
1240.0168
1250.934
1260.703
1270.77
1280.228
1290.963
130.0989
1300.431
1310.916
1320.937
1330.0788
1340.458
1350.42
1360.156
1370.136
1380.97
1390.0824
140.319
1400.221
1410.758
1420.606
1430.226
1440.491
1450.571
1460.656
1470.242
1480.411
1490.841
150.404
1500.0326
1510.264
1520.179
1530.417
1540.966
1550.0127
1560.173
1570.18
1580.133
1590.781
160.146
1600.312
1610.532
1620.934
1630.804
1640.00787
1650.817
1660.289
1670.308
1680.397
1690.0169
170.808
180.144
190.7
20.711
200.996
210.0726
220.923
230.837
240.621
250.762
260.172
270.848
280.622
290.00509
30.281
300.649
310.634
320.035
330.305
340.166
350.335
360.837
370.92
380.868
390.963
40.372
400.255
410.0927
420.244
430.452
440.313
450.253
460.501
470.619
480.544
490.361
50.849
500.96
510.585
520.51
530.466
540.996
550.796
560.495
570.0624
580.238
590.601
60.918
600.439
610.929
620.577
630.641
640.848
650.911
660.415
670.78
680.861
690.971
70.956
700.268
710.00743
720.691
730.338
740.0135
750.742
760.433
770.212
780.44
790.0574
80.0572
800.114
810.0534
821
830.796
840.49
850.55
860.0649
870.192
880.506
890.354
90.333
900.436
910.596
920.561
930.751
940.472
950.801
960.647
970.88
980.099
990.0417



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: CNhs13067


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
4 (disease)
7 (disease of anatomical entity)

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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