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FF:10093-102C3: 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 16:48, 29 March 2012


Name:salivary gland, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesalivary gland
dev stage16-60 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number8101369A-13
catalog numberCat: 636643 Lot: 8101369A-13
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
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-0.407
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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: CNhs11677

Jaspar motifP-value
MA0002.20.212
MA0003.10.222
MA0004.10.558
MA0006.10.194
MA0007.10.561
MA0009.10.0476
MA0014.10.688
MA0017.10.333
MA0018.20.00194
MA0019.10.775
MA0024.16.17612e-4
MA0025.10.835
MA0027.10.376
MA0028.10.0219
MA0029.10.585
MA0030.10.00156
MA0031.10.0984
MA0035.20.898
MA0038.10.734
MA0039.20.024
MA0040.10.529
MA0041.10.813
MA0042.10.288
MA0043.10.0242
MA0046.10.933
MA0047.22.0805e-4
MA0048.12.63977e-5
MA0050.10.0584
MA0051.10.347
MA0052.11.39033e-4
MA0055.10.00425
MA0057.10.444
MA0058.10.253
MA0059.10.233
MA0060.10.0319
MA0061.10.0786
MA0062.20.00925
MA0065.20.821
MA0066.10.16
MA0067.10.00833
MA0068.10.629
MA0069.10.97
MA0070.10.6
MA0071.10.53
MA0072.10.384
MA0073.10.756
MA0074.10.758
MA0076.10.0259
MA0077.10.135
MA0078.10.197
MA0079.20.116
MA0080.20.646
MA0081.10.00468
MA0083.10.633
MA0084.10.652
MA0087.10.149
MA0088.10.403
MA0090.10.61
MA0091.10.293
MA0092.10.605
MA0093.10.555
MA0099.22.83573e-14
MA0100.10.00975
MA0101.10.0182
MA0102.20.0692
MA0103.19.62442e-7
MA0104.20.0826
MA0105.10.00264
MA0106.10.768
MA0107.10.0766
MA0108.25.83093e-7
MA0111.10.576
MA0112.20.0352
MA0113.10.473
MA0114.10.923
MA0115.10.727
MA0116.10.741
MA0117.10.143
MA0119.10.304
MA0122.10.846
MA0124.10.464
MA0125.10.543
MA0131.10.0649
MA0135.10.411
MA0136.10.459
MA0137.20.406
MA0138.20.0246
MA0139.10.457
MA0140.10.321
MA0141.10.0825
MA0142.10.95
MA0143.10.209
MA0144.10.704
MA0145.10.00869
MA0146.10.345
MA0147.10.0598
MA0148.15.36577e-4
MA0149.10.683
MA0150.15.80506e-4
MA0152.10.459
MA0153.10.031
MA0154.10.455
MA0155.10.75
MA0156.10.485
MA0157.10.0608
MA0159.10.299
MA0160.10.129
MA0162.10.738
MA0163.10.00557
MA0164.10.0557
MA0258.10.159
MA0259.10.216



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: CNhs11677

Novel motifP-value
10.918
100.0316
1000.759
1010.706
1020.613
1030.745
1040.349
1050.345
1060.874
1070.243
1080.684
1090.989
110.924
1100.555
1110.534
1120.313
1130.257
1140.914
1150.712
1160.811
1170.125
1180.232
1190.355
120.598
1200.124
1210.824
1220.262
1230.182
1240.984
1250.442
1260.0825
1270.559
1280.475
1290.755
130.719
1300.722
1310.664
1320.0507
1330.178
1340.00132
1350.958
1360.682
1370.649
1380.304
1390.645
140.363
1400.885
1410.912
1420.6
1430.205
1440.0649
1450.202
1460.00639
1470.874
1480.972
1490.0969
150.804
1500.667
1510.691
1520.37
1530.926
1540.972
1550.868
1560.134
1570.333
1580.774
1590.0585
160.584
1600.733
1610.958
1620.266
1630.428
1640.123
1650.673
1660.911
1670.0607
1680.202
1690.0433
170.617
180.204
190.254
20.0153
200.0526
210.32
220.522
230.368
240.79
250.953
260.875
270.297
280.651
290.649
30.659
300.00638
310.751
320.814
330.919
340.748
350.587
360.00705
370.439
380.329
390.363
40.592
400.695
410.186
420.762
430.963
440.725
450.0929
460.765
470.663
480.959
490.827
50.153
500.637
510.799
520.202
530.516
540.934
550.46
560.601
570.717
580.371
590.414
60.357
600.279
610.954
620.814
630.243
640.927
650.305
660.418
670.676
680.467
690.178
70.489
700.404
710.318
720.77
730.835
740.568
750.341
760.108
770.00196
780.354
790.113
80.911
800.195
810.334
820.6
830.623
840.56
850.213
860.87
870.887
880.88
890.294
90.698
900.845
910.876
920.192
930.885
940.116
950.0111
960.532
970.62
980.683
990.354



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: CNhs11677


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)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0002050 (embryonic structure)
0002530 (gland)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003293 (gland of oral region)
0003294 (gland of foregut)
0003408 (gland of gut)
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)
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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