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Revision as of 20:45, 15 May 2017

Name:salivary acinar cells, donor2
Species:Human (Homo sapiens)
Library ID:CNhs12811
Sample type:primary cells
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueparotid gland
dev stageNA
sexfemale
age49
cell typesalivary acinar cell
cell lineNA
companyNA
collaborationSwati Pradhan
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005311
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12811 CAGE DRX008574 DRR009446
Accession ID Hg19

Library idBAMCTSS
CNhs12811 DRZ000871 DRZ002256
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-penis0.27
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-0.154
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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



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: CNhs12811

Jaspar motifP-value
MA0002.22.68031e-4
MA0003.10.139
MA0004.10.486
MA0006.10.0812
MA0007.10.121
MA0009.10.576
MA0014.10.287
MA0017.10.0408
MA0018.26.00063e-5
MA0019.10.181
MA0024.10.408
MA0025.10.0014
MA0027.10.0938
MA0028.10.637
MA0029.10.443
MA0030.10.887
MA0031.10.25
MA0035.20.0611
MA0038.10.0105
MA0039.20.514
MA0040.10.099
MA0041.10.887
MA0042.10.484
MA0043.10.00118
MA0046.10.201
MA0047.20.728
MA0048.10.11
MA0050.12.12798e-12
MA0051.13.47645e-8
MA0052.10.0104
MA0055.10.187
MA0057.10.422
MA0058.10.144
MA0059.10.0505
MA0060.10.00262
MA0061.11.33534e-5
MA0062.23.22368e-5
MA0065.20.11
MA0066.10.659
MA0067.10.0244
MA0068.10.0114
MA0069.10.368
MA0070.10.948
MA0071.10.026
MA0072.10.242
MA0073.10.699
MA0074.10.418
MA0076.10.271
MA0077.10.762
MA0078.10.862
MA0079.20.282
MA0080.21.13347e-13
MA0081.10.00245
MA0083.10.0536
MA0084.10.594
MA0087.10.927
MA0088.10.625
MA0090.10.0191
MA0091.10.0927
MA0092.10.0524
MA0093.10.278
MA0099.21.32801e-4
MA0100.10.326
MA0101.12.09965e-6
MA0102.20.789
MA0103.10.185
MA0104.20.0521
MA0105.10.00185
MA0106.12.06464e-16
MA0107.13.87041e-6
MA0108.20.894
MA0111.10.919
MA0112.20.0753
MA0113.10.00284
MA0114.10.18
MA0115.10.227
MA0116.10.0525
MA0117.10.018
MA0119.10.173
MA0122.10.394
MA0124.10.449
MA0125.10.48
MA0131.10.907
MA0135.10.28
MA0136.13.8202e-12
MA0137.20.0219
MA0138.20.61
MA0139.10.016
MA0140.10.022
MA0141.10.241
MA0142.10.131
MA0143.10.347
MA0144.10.0632
MA0145.10.972
MA0146.10.762
MA0147.10.0813
MA0148.10.0466
MA0149.10.72
MA0150.16.90444e-5
MA0152.10.922
MA0153.10.369
MA0154.10.00263
MA0155.10.285
MA0156.12.66494e-13
MA0157.10.72
MA0159.10.126
MA0160.10.123
MA0162.10.558
MA0163.10.00359
MA0164.10.422
MA0258.10.0798
MA0259.10.6



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: CNhs12811

Novel motifP-value
10.46
100.127
1000.739
1010.435
1020.373
1030.681
1040.837
1050.574
1060.763
1070.663
1080.713
1090.552
110.456
1100.801
1110.66
1120.507
1130.0175
1140.932
1150.319
1160.87
1170.448
1180.768
1190.844
120.0833
1200.113
1210.672
1220.251
1230.112
1240.00295
1250.956
1260.512
1270.783
1280.359
1290.729
130.386
1300.257
1310.863
1320.0115
1330.0936
1340.282
1350.213
1360.0352
1370.0204
1380.511
1390.594
140.786
1400.278
1410.424
1420.512
1430.0183
1440.383
1450.957
1460.956
1470.385
1480.179
1490.932
150.129
1500.732
1510.987
1520.167
1530.579
1540.643
1550.277
1560.245
1570.923
1580.0514
1590.31
160.467
1600.906
1610.19
1620.139
1630.956
1640.896
1650.443
1660.104
1670.634
1680.946
1690.823
170.918
180.318
190.443
20.432
200.391
210.242
220.58
230.139
240.107
250.252
260.752
270.596
280.978
290.46
30.914
300.568
310.717
320.931
330.797
340.0614
350.229
360.00527
370.811
380.753
390.365
40.104
400.0197
410.0993
420.489
430.272
440.149
450.552
460.609
470.225
480.921
490.0429
50.182
500.72
510.847
520.511
530.0507
540.816
550.578
560.821
570.757
580.44
590.194
60.544
600.544
610.186
620.188
630.783
640.279
650.907
660.265
670.26
680.698
690.164
70.187
700.636
710.664
720.774
730.168
740.0137
750.475
760.566
770.678
780.427
790.993
80.412
800.209
810.874
820.467
830.186
840.0308
850.886
860.379
870.422
880.89
890.881
90.313
900.616
910.921
920.915
930.771
940.171
950.0716
960.347
970.894
980.791
990.395



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: CNhs12811


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000151 (secretory cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000150 (glandular epithelial cell)
0000154 (protein secreting cell)
0000255 (eukaryotic cell)
0000622 (acinar cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0002623 (acinar cell of salivary gland)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001044 (saliva-secreting gland)
0000033 (head)
0001007 (digestive system)
0004121 (ectoderm-derived structure)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000161 (orifice)
0001444 (subdivision of head)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003293 (gland of oral region)
0003294 (gland of foregut)
0002365 (exocrine gland)
0000464 (anatomical space)
0002530 (gland)
0010047 (oral gland)
0003408 (gland of gut)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0001004 (respiratory system)
0000153 (anterior region of body)
0007811 (craniocervical region)
0000165 (mouth)
0001041 (foregut)
0000166 (oral opening)
0000167 (oral cavity)
0002330 (exocrine system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000278 (human salivary acinar cell sample)

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
CL:0000223 (endodermal cell)

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