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{{f5samples
{{f5samples
|id=FF:10202-103F4
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000153,UBERON:0000161,UBERON:0000165,UBERON:0000166,UBERON:0000167,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000930,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001044,UBERON:0001048,UBERON:0001062,UBERON:0001444,UBERON:0001555,UBERON:0001736,UBERON:0001829,UBERON:0002050,UBERON:0002330,UBERON:0002365,UBERON:0002530,UBERON:0002532,UBERON:0002553,UBERON:0003104,UBERON:0003293,UBERON:0003294,UBERON:0003408,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005423,UBERON:0006298,UBERON:0007023,UBERON:0007026,UBERON:0009142
|name=submaxillary gland, adult
|sample_id=10202
|rna_tube_id=103F4
|rna_box=103
|rna_position=F4
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=Biochain
|rna_lot_number=
|rna_catalog_number=R1234165-10
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=
|sample_donor(cell lot)=
|sample_sex=24
|sample_age=M
|sample_ethnicity=
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=
|rna_extraction_protocol=
|rna_weight_ug=10
|rna_concentration=2.15
|sample_note=
|profile_hcage=CNhs12852,LSID973,release012,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
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|creation_date=
|def=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10202-103F4
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010202
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010202
|name=submaxillary gland, adult
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12852,LSID973,release012,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=103
|rna_catalog_number=R1234165-10
|rna_concentration=2.15
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=F4
|rna_rin=
|rna_sample_type=
|rna_tube_id=103F4
|rna_weight_ug=10
|sample_age=M
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_lot=NA
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=
|sample_company=Biochain
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10202
|sample_note=
|sample_sex=24
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=
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}}
}}

Revision as of 14:03, 21 March 2012


Name:submaxillary 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
sex24
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 numberR1234165-10
sample typeNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]





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-penis0.0288
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-0.367
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs12852

Jaspar motifP-value
MA0002.20.5
MA0003.10.116
MA0004.10.294
MA0006.10.124
MA0007.10.447
MA0009.10.441
MA0014.10.886
MA0017.10.352
MA0018.23.49115e-6
MA0019.10.314
MA0024.15.94766e-4
MA0025.10.292
MA0027.10.913
MA0028.15.56928e-4
MA0029.10.449
MA0030.10.275
MA0031.10.54
MA0035.20.397
MA0038.10.0385
MA0039.20.198
MA0040.10.844
MA0041.10.803
MA0042.10.873
MA0043.15.46074e-5
MA0046.10.144
MA0047.20.149
MA0048.18.96801e-5
MA0050.10.965
MA0051.10.55
MA0052.14.54366e-5
MA0055.12.76599e-4
MA0057.10.475
MA0058.10.0576
MA0059.10.092
MA0060.11.03488e-4
MA0061.10.0161
MA0062.21.20363e-4
MA0065.20.862
MA0066.10.311
MA0067.16.96609e-4
MA0068.10.521
MA0069.10.735
MA0070.10.306
MA0071.10.708
MA0072.10.202
MA0073.10.775
MA0074.10.953
MA0076.13.121e-4
MA0077.10.477
MA0078.10.374
MA0079.20.126
MA0080.20.669
MA0081.19.67582e-4
MA0083.10.712
MA0084.10.845
MA0087.10.112
MA0088.10.277
MA0090.10.959
MA0091.10.261
MA0092.10.985
MA0093.10.243
MA0099.22.09223e-25
MA0100.10.0051
MA0101.10.00182
MA0102.20.165
MA0103.11.59246e-7
MA0104.20.00764
MA0105.12.09783e-4
MA0106.10.168
MA0107.10.00413
MA0108.20.00615
MA0111.10.538
MA0112.20.00984
MA0113.10.885
MA0114.10.653
MA0115.10.478
MA0116.10.22
MA0117.10.0885
MA0119.10.435
MA0122.10.71
MA0124.10.745
MA0125.10.885
MA0131.10.0541
MA0135.10.446
MA0136.10.154
MA0137.20.325
MA0138.20.2
MA0139.10.815
MA0140.10.124
MA0141.10.137
MA0142.10.635
MA0143.10.391
MA0144.10.989
MA0145.10.00976
MA0146.10.397
MA0147.10.00628
MA0148.10.305
MA0149.10.168
MA0150.11.36508e-7
MA0152.10.159
MA0153.10.488
MA0154.10.96
MA0155.10.323
MA0156.10.227
MA0157.10.941
MA0159.10.569
MA0160.10.403
MA0162.10.406
MA0163.10.00248
MA0164.10.465
MA0258.10.0546
MA0259.10.0762



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: CNhs12852

Novel motifP-value
10.873
100.0502
1000.749
1010.791
1020.596
1030.93
1040.161
1050.0546
1060.41
1070.0477
1080.1
1090.381
110.807
1100.465
1110.659
1120.158
1130.469
1140.817
1150.622
1160.271
1170.14
1180.0843
1190.159
120.316
1200.068
1210.994
1220.51
1230.545
1240.521
1250.788
1260.0875
1270.369
1280.0691
1290.616
130.461
1300.445
1310.866
1320.0584
1330.232
1340.0156
1350.867
1360.81
1370.509
1380.343
1390.212
140.446
1400.4
1410.431
1420.978
1430.419
1440.569
1450.314
1460.0846
1470.689
1480.628
1490.298
150.454
1500.985
1510.578
1520.205
1530.685
1540.814
1550.924
1560.329
1570.845
1580.461
1590.0285
160.619
1600.666
1610.637
1620.214
1630.257
1640.277
1650.719
1660.673
1670.0445
1680.301
1690.1
170.679
180.353
190.245
20.0149
200.0122
210.842
220.755
230.591
240.531
250.884
260.82
270.214
280.958
290.297
30.601
300.007
310.572
320.68
330.94
340.713
350.675
360.00384
370.487
380.524
390.413
40.575
400.153
410.0923
420.411
430.941
440.106
450.134
460.935
470.726
480.904
490.605
50.336
500.723
510.81
520.193
530.982
540.904
550.45
560.754
570.758
580.559
590.198
60.433
600.313
610.55
620.888
630.387
640.85
650.516
660.103
670.502
680.274
690.394
70.823
700.311
710.246
720.362
730.757
740.901
750.15
760.117
770.00191
780.277
790.66
80.667
800.956
810.0467
820.657
830.476
840.638
850.0536
860.693
870.973
880.704
890.181
90.912
900.892
910.668
920.395
930.204
940.0659
950.0342
960.283
970.218
980.593
990.234



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: CNhs12852


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)
0001555 (digestive tract)
0001736 (submandibular gland)
0001829 (major salivary 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)
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)
0006298 (submandibular gland primordium)
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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