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FF:10209-103G2: 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 17:26, 29 March 2012


Name:throat, adult
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sex28
ageM
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberR1234263-10
sample typeNA
extraction protocol (Details)NA
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-0.0605
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-0.0838
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0.432
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: CNhs12858

Jaspar motifP-value
MA0002.20.211
MA0003.10.0628
MA0004.10.0218
MA0006.10.1
MA0007.10.334
MA0009.10.879
MA0014.10.953
MA0017.10.162
MA0018.20.0398
MA0019.10.271
MA0024.10.0623
MA0025.10.933
MA0027.10.837
MA0028.13.38445e-6
MA0029.10.639
MA0030.10.055
MA0031.10.442
MA0035.20.277
MA0038.10.0182
MA0039.20.239
MA0040.10.808
MA0041.10.0979
MA0042.10.187
MA0043.10.0346
MA0046.10.0491
MA0047.20.0535
MA0048.10.00152
MA0050.10.0398
MA0051.10.145
MA0052.12.02471e-27
MA0055.18.25402e-4
MA0057.10.304
MA0058.10.0028
MA0059.10.00325
MA0060.10.00607
MA0061.13.72417e-4
MA0062.21.94914e-9
MA0065.20.367
MA0066.10.807
MA0067.10.0541
MA0068.10.0637
MA0069.10.447
MA0070.10.503
MA0071.10.777
MA0072.10.0856
MA0073.10.876
MA0074.10.926
MA0076.13.18044e-6
MA0077.10.61
MA0078.10.27
MA0079.20.127
MA0080.20.0309
MA0081.10.0176
MA0083.10.0318
MA0084.10.679
MA0087.10.284
MA0088.10.125
MA0090.10.42
MA0091.10.259
MA0092.10.237
MA0093.10.0146
MA0099.22.45928e-15
MA0100.10.0914
MA0101.14.60738e-4
MA0102.20.0751
MA0103.10.00161
MA0104.29.43357e-4
MA0105.10.00113
MA0106.10.507
MA0107.12.50818e-4
MA0108.28.5835e-26
MA0111.10.487
MA0112.20.00594
MA0113.10.0308
MA0114.10.74
MA0115.10.211
MA0116.10.192
MA0117.10.257
MA0119.10.797
MA0122.10.0656
MA0124.10.915
MA0125.10.667
MA0131.10.0219
MA0135.10.345
MA0136.10.00395
MA0137.20.406
MA0138.20.148
MA0139.10.538
MA0140.10.31
MA0141.10.284
MA0142.10.07
MA0143.10.151
MA0144.10.936
MA0145.10.0124
MA0146.10.48
MA0147.19.27456e-4
MA0148.10.106
MA0149.10.11
MA0150.16.72225e-4
MA0152.10.883
MA0153.10.673
MA0154.10.693
MA0155.10.093
MA0156.12.40547e-5
MA0157.10.798
MA0159.10.314
MA0160.10.446
MA0162.10.105
MA0163.10.0289
MA0164.10.709
MA0258.10.0894
MA0259.10.0152



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: CNhs12858

Novel motifP-value
10.811
100.106
1000.329
1010.111
1020.833
1030.4
1040.713
1050.718
1060.423
1070.0831
1080.218
1090.828
110.84
1100.689
1110.46
1120.0793
1130.898
1140.171
1150.0627
1160.468
1170.192
1180.0296
1190.282
120.774
1200.716
1210.518
1220.391
1230.019
1240.323
1250.828
1260.138
1270.758
1280.189
1290.368
130.375
1300.745
1310.408
1320.043
1331.0711e-4
1340.0048
1350.0636
1360.654
1370.326
1380.512
1390.419
140.505
1400.888
1410.964
1420.567
1430.00506
1440.671
1450.952
1460.686
1470.0203
1480.906
1490.0124
150.368
1500.884
1510.406
1520.102
1530.485
1540.64
1550.611
1560.111
1570.907
1580.0762
1590.841
160.346
1600.705
1610.692
1620.503
1630.106
1640.197
1650.0359
1660.0884
1670.0614
1680.144
1690.0481
170.879
180.0812
190.126
20.00823
200.0546
210.643
220.139
230.331
240.567
250.835
260.536
270.398
280.974
290.184
30.78
300.00751
310.766
320.226
330.506
340.278
350.597
360.0126
370.941
380.779
390.199
40.655
400.234
410.481
420.461
430.672
440.0312
450.027
460.84
470.571
480.579
490.435
50.644
500.387
510.703
520.069
530.683
540.924
550.978
560.889
570.383
580.966
590.16
60.728
600.211
610.612
620.805
630.324
640.827
650.479
660.00837
670.241
680.23
690.379
70.682
700.665
710.363
720.637
730.573
740.126
750.301
760.0105
770.0105
780.906
790.472
80.931
800.638
810.696
820.417
830.719
840.906
850.112
860.714
870.847
880.63
890.0956
90.459
900.0659
910.0976
920.407
930.95
940.0791
950.395
960.64
970.813
980.999
990.112



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: CNhs12858


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)
0001062 (anatomical entity)
0007023 (adult organism)

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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