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FF:10198-103E9: 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:gall bladder, 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
sex57
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 numberR1234118-10
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-0.0756
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-0.281
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12848

Jaspar motifP-value
MA0002.20.618
MA0003.10.12
MA0004.10.0856
MA0006.10.141
MA0007.10.952
MA0009.10.27
MA0014.10.467
MA0017.10.0298
MA0018.20.864
MA0019.10.0349
MA0024.10.00661
MA0025.10.326
MA0027.10.682
MA0028.14.57281e-4
MA0029.10.755
MA0030.15.63764e-4
MA0031.10.0764
MA0035.20.159
MA0038.10.218
MA0039.20.677
MA0040.10.737
MA0041.10.073
MA0042.10.497
MA0043.10.399
MA0046.11.93065e-33
MA0047.22.95156e-4
MA0048.10.0696
MA0050.10.33
MA0051.10.638
MA0052.10.00479
MA0055.10.00239
MA0057.10.608
MA0058.10.0515
MA0059.10.00394
MA0060.10.0497
MA0061.10.002
MA0062.21.24653e-4
MA0065.20.96
MA0066.10.0166
MA0067.10.148
MA0068.10.164
MA0069.10.652
MA0070.10.666
MA0071.10.232
MA0072.10.0737
MA0073.10.811
MA0074.10.426
MA0076.13.5479e-4
MA0077.10.946
MA0078.10.298
MA0079.20.0731
MA0080.20.338
MA0081.10.0965
MA0083.18.41672e-6
MA0084.10.806
MA0087.10.114
MA0088.10.0442
MA0090.10.0686
MA0091.10.613
MA0092.10.749
MA0093.10.115
MA0099.21.15516e-9
MA0100.10.039
MA0101.10.00973
MA0102.20.707
MA0103.10.0338
MA0104.20.00109
MA0105.12.8215e-5
MA0106.10.112
MA0107.10.0101
MA0108.27.73109e-15
MA0111.10.629
MA0112.20.568
MA0113.10.587
MA0114.10.282
MA0115.10.992
MA0116.10.00422
MA0117.10.292
MA0119.10.613
MA0122.10.591
MA0124.10.938
MA0125.10.99
MA0131.10.217
MA0135.10.119
MA0136.10.493
MA0137.20.155
MA0138.20.0412
MA0139.10.687
MA0140.10.284
MA0141.10.334
MA0142.10.0756
MA0143.10.0819
MA0144.10.0502
MA0145.10.0554
MA0146.10.914
MA0147.15.7836e-4
MA0148.11.83981e-4
MA0149.10.165
MA0150.11.02321e-4
MA0152.10.976
MA0153.11.57411e-19
MA0154.10.273
MA0155.10.262
MA0156.10.0763
MA0157.10.884
MA0159.10.281
MA0160.10.947
MA0162.10.75
MA0163.18.60988e-5
MA0164.10.265
MA0258.10.447
MA0259.10.0205



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: CNhs12848

Novel motifP-value
10.045
100.0466
1000.178
1010.205
1020.325
1030.136
1040.955
1050.674
1060.566
1070.118
1080.872
1090.41
110.27
1100.215
1110.0175
1120.76
1130.831
1140.126
1150.554
1160.737
1170.0319
1180.131
1190.921
120.817
1200.0778
1210.83
1220.808
1230.0794
1240.171
1250.0166
1260.967
1270.275
1280.192
1290.29
130.0411
1300.898
1310.317
1320.0443
1330.0618
1340.044
1350.399
1360.829
1370.487
1380.948
1390.244
140.946
1400.202
1410.169
1420.715
1430.0291
1440.853
1450.508
1460.94
1470.763
1480.427
1490.187
150.119
1500.777
1510.369
1520.0487
1530.555
1540.552
1550.761
1560.75
1570.727
1580.44
1590.443
160.367
1600.833
1610.276
1620.915
1630.703
1640.1
1650.92
1660.39
1670.032
1680.405
1690.339
170.944
180.0136
190.387
20.021
200.0774
210.214
220.643
230.402
240.43
250.367
260.544
270.574
280.588
290.0315
30.112
300.0258
310.881
320.344
330.422
340.264
350.398
360.0237
370.481
380.987
390.385
40.348
400.163
410.036
420.153
430.349
440.984
450.199
460.194
470.171
480.28
490.094
50.263
500.47
510.849
520.149
530.831
540.951
550.678
560.694
570.0636
580.733
590.589
60.473
600.48
610.866
620.456
630.97
640.464
650.677
660.00977
670.276
680.412
690.816
70.515
700.138
710.0279
720.855
730.961
740.611
750.0147
760.0149
770.0407
780.631
790.725
80.385
800.311
810.194
820.853
830.942
840.994
850.396
860.787
870.844
880.991
890.463
90.387
900.0118
910.92
920.895
930.0763
940.00482
950.15
960.204
970.872
980.108
990.125



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: CNhs12848


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
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000119 (cell layer)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001007 (digestive system)
0001041 (foregut)
0001062 (anatomical entity)
0001173 (biliary tree)
0001555 (digestive tract)
0002050 (embryonic structure)
0002075 (viscus)
0002100 (trunk)
0002110 (gallbladder)
0002294 (biliary system)
0002323 (body cavity)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003914 (epithelial tube)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004458 (body cavity or lining)
0004912 (biliary bud)
0004921 (subdivision of digestive tract)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0007023 (adult organism)
0007026 (primitive gut)
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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