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FF:10199-103F1: 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:parotid gland, 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
sex23
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 numberR1234190-50
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-9.34345e-4
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-0.423
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12849

Jaspar motifP-value
MA0002.20.0617
MA0003.10.0773
MA0004.10.527
MA0006.10.0957
MA0007.10.942
MA0009.10.361
MA0014.10.929
MA0017.10.0218
MA0018.21.32328e-4
MA0019.10.568
MA0024.10.0443
MA0025.10.817
MA0027.10.704
MA0028.10.0104
MA0029.10.655
MA0030.10.145
MA0031.10.567
MA0035.20.458
MA0038.10.203
MA0039.20.885
MA0040.10.838
MA0041.10.147
MA0042.10.413
MA0043.10.00174
MA0046.10.444
MA0047.20.129
MA0048.10.00506
MA0050.10.392
MA0051.10.862
MA0052.10.00639
MA0055.10.0432
MA0057.10.234
MA0058.10.246
MA0059.10.614
MA0060.10.0159
MA0061.10.438
MA0062.21.55112e-5
MA0065.20.225
MA0066.10.617
MA0067.17.79892e-4
MA0068.10.229
MA0069.10.758
MA0070.10.76
MA0071.10.986
MA0072.10.655
MA0073.10.287
MA0074.10.996
MA0076.10.00486
MA0077.10.423
MA0078.10.488
MA0079.20.49
MA0080.20.166
MA0081.10.0227
MA0083.10.295
MA0084.10.88
MA0087.10.102
MA0088.10.892
MA0090.10.513
MA0091.10.778
MA0092.10.298
MA0093.10.493
MA0099.22.6261e-12
MA0100.10.0615
MA0101.10.439
MA0102.20.188
MA0103.11.3032e-6
MA0104.20.0816
MA0105.10.039
MA0106.10.738
MA0107.10.297
MA0108.20.00482
MA0111.10.978
MA0112.20.00802
MA0113.10.115
MA0114.10.782
MA0115.10.989
MA0116.10.559
MA0117.10.376
MA0119.10.451
MA0122.10.868
MA0124.10.455
MA0125.10.299
MA0131.10.161
MA0135.10.729
MA0136.10.00452
MA0137.22.30234e-10
MA0138.20.118
MA0139.15.57675e-7
MA0140.10.758
MA0141.10.236
MA0142.10.479
MA0143.10.00467
MA0144.11.6874e-10
MA0145.10.0993
MA0146.10.582
MA0147.10.0695
MA0148.10.22
MA0149.10.965
MA0150.18.32031e-4
MA0152.10.938
MA0153.10.116
MA0154.10.257
MA0155.10.756
MA0156.10.213
MA0157.10.471
MA0159.10.225
MA0160.10.718
MA0162.10.972
MA0163.10.0424
MA0164.10.395
MA0258.10.188
MA0259.10.101



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: CNhs12849

Novel motifP-value
10.459
100.278
1000.91
1010.828
1020.805
1030.588
1040.279
1050.703
1060.127
1070.0898
1080.305
1090.836
110.71
1100.726
1110.463
1120.171
1130.706
1140.594
1150.992
1160.841
1170.415
1180.522
1190.304
120.108
1200.0274
1210.479
1220.478
1230.798
1240.737
1250.826
1260.0852
1270.388
1280.0848
1290.559
130.715
1300.0741
1310.874
1320.219
1330.0867
1340.154
1350.534
1360.778
1370.887
1380.657
1390.383
140.552
1400.798
1410.355
1420.524
1430.806
1440.748
1450.528
1460.204
1470.761
1480.916
1490.181
150.487
1500.801
1510.52
1520.047
1530.0786
1540.97
1550.644
1560.168
1570.314
1580.62
1590.799
160.439
1600.501
1610.733
1620.185
1630.8
1640.269
1650.932
1660.907
1670.548
1680.234
1690.0368
170.4
180.953
190.293
25.35026e-6
200.321
210.351
220.317
230.35
240.458
250.985
260.384
270.156
280.978
290.837
30.941
300.00871
310.373
329.13836e-8
330.712
340.768
350.957
360.00347
370.916
380.43
390.217
40.533
400.886
410.294
420.8
430.554
440.0299
450.0881
460.603
470.996
480.782
490.859
50.0524
500.297
510.734
520.224
530.959
540.566
550.632
560.539
570.64
580.565
590.0398
60.8
600.145
610.903
620.686
630.112
640.851
650.294
660.379
670.686
680.406
690.609
70.538
700.132
710.884
720.735
730.221
740.663
750.894
760.266
770.142
780.426
790.411
80.462
800.803
810.637
820.281
830.639
840.651
850.0283
860.651
870.733
880.786
890.193
90.696
900.415
910.652
920.257
930.902
940.194
950.288
960.776
970.646
980.67
990.265



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: CNhs12849


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
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000153 (anterior region of body)
0000161 (orifice)
0000165 (mouth)
0000166 (oral opening)
0000167 (oral cavity)
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)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000930 (stomodeum)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001044 (saliva-secreting gland)
0001048 (primordium)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0001555 (digestive tract)
0001567 (cheek)
0001829 (major salivary gland)
0001831 (parotid gland)
0002050 (embryonic structure)
0002330 (exocrine system)
0002365 (exocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003293 (gland of oral region)
0003294 (gland of foregut)
0003408 (gland of gut)
0004089 (midface)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007026 (primitive gut)
0008801 (parotid gland 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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