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FF:10061-101H7: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 16:52, 29 March 2012


Name:throat, fetal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuethroat
dev stage25 weeks fetus
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB212133
catalog numberCat:RtHFN: Throat
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-penis0.0448
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-lymphoma0.0813
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0.234
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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: CNhs11770

Jaspar motifP-value
MA0002.23.67495e-5
MA0003.10.353
MA0004.10.0271
MA0006.10.859
MA0007.10.139
MA0009.10.0562
MA0014.10.666
MA0017.10.0821
MA0018.20.487
MA0019.10.579
MA0024.10.274
MA0025.10.187
MA0027.10.963
MA0028.10.0106
MA0029.10.371
MA0030.10.461
MA0031.10.679
MA0035.20.0276
MA0038.10.87
MA0039.20.384
MA0040.10.524
MA0041.10.474
MA0042.10.932
MA0043.10.053
MA0046.10.00801
MA0047.20.85
MA0048.10.195
MA0050.10.0188
MA0051.10.0756
MA0052.18.46409e-14
MA0055.10.0411
MA0057.10.792
MA0058.10.0239
MA0059.10.00545
MA0060.10.823
MA0061.17.7185e-5
MA0062.21.53751e-5
MA0065.20.00257
MA0066.10.0641
MA0067.10.0451
MA0068.10.00851
MA0069.10.39
MA0070.10.752
MA0071.10.358
MA0072.10.242
MA0073.10.456
MA0074.10.204
MA0076.10.0166
MA0077.10.827
MA0078.10.548
MA0079.20.791
MA0080.21.82208e-7
MA0081.10.0372
MA0083.10.644
MA0084.10.087
MA0087.10.107
MA0088.10.0362
MA0090.10.422
MA0091.10.652
MA0092.10.482
MA0093.10.0418
MA0099.22.08879e-24
MA0100.10.943
MA0101.11.23014e-4
MA0102.20.00551
MA0103.10.965
MA0104.20.00306
MA0105.14.28877e-9
MA0106.10.0045
MA0107.11.89891e-4
MA0108.22.53625e-9
MA0111.10.726
MA0112.20.0114
MA0113.10.976
MA0114.10.0161
MA0115.10.296
MA0116.13.69892e-5
MA0117.10.13
MA0119.10.615
MA0122.10.291
MA0124.10.595
MA0125.10.22
MA0131.10.831
MA0135.10.512
MA0136.16.01483e-10
MA0137.20.645
MA0138.20.907
MA0139.10.0887
MA0140.10.0113
MA0141.10.0169
MA0142.10.048
MA0143.10.339
MA0144.10.431
MA0145.10.637
MA0146.10.0739
MA0147.10.00119
MA0148.10.885
MA0149.10.0237
MA0150.15.40057e-9
MA0152.10.0278
MA0153.10.982
MA0154.10.00129
MA0155.10.587
MA0156.11.35096e-7
MA0157.10.403
MA0159.10.0823
MA0160.10.00872
MA0162.10.37
MA0163.12.90427e-8
MA0164.10.429
MA0258.10.072
MA0259.10.151



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: CNhs11770

Novel motifP-value
10.0546
100.0476
1000.408
1010.772
1020.577
1030.0595
1040.551
1050.764
1060.16
1070.978
1080.935
1090.00253
110.0694
1100.166
1110.0604
1120.737
1130.0199
1140.00247
1150.43
1160.86
1170.0147
1180.0467
1190.242
120.426
1200.248
1210.9
1220.112
1230.139
1240.19
1250.302
1260.672
1270.126
1280.534
1290.674
130.215
1300.798
1310.568
1320.0795
1330.302
1340.472
1350.47
1360.325
1370.502
1380.452
1390.137
140.737
1400.652
1410.273
1420.287
1431.3921e-4
1440.85
1450.663
1460.472
1470.315
1480.0574
1490.658
150.0563
1500.42
1510.477
1520.46
1530.606
1540.809
1550.164
1560.626
1570.804
1580.414
1590.81
160.315
1600.522
1610.373
1620.262
1630.0399
1640.208
1650.605
1660.251
1670.0861
1680.829
1690.0117
170.123
180.00571
190.777
20.713
200.139
210.484
220.367
230.576
240.188
250.61
260.0202
270.619
280.551
290.0435
30.126
300.194
310.736
320.191
330.292
340.783
350.183
360.0186
370.0358
380.31
390.734
40.717
400.0643
410.104
420.204
430.047
440.811
450.903
460.0722
470.0424
480.108
490.0495
50.331
500.889
510.345
520.915
530.733
540.382
550.333
560.446
570.265
580.323
590.167
60.759
600.526
610.13
620.22
630.484
640.222
650.28
660.0545
670.415
680.787
690.841
70.623
700.0325
710.0191
720.158
730.102
740.468
750.0152
760.125
770.509
780.0989
790.649
80.0904
800.896
810.404
820.314
830.473
840.781
850.336
860.176
870.00227
880.78
890.526
90.8
900.0868
910.673
920.376
930.974
940.0446
950.00647
960.277
970.965
980.117
990.55



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: CNhs11770


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

UBERON: Anatomy
0000061 (anatomical structure)
0000341 (throat)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000922 (embryo)
0001062 (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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