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{{f5samples
{{f5samples
|id=FF:10205-103F7
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000055,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000926,UBERON:0000946,UBERON:0000948,UBERON:0001009,UBERON:0001048,UBERON:0001062,UBERON:0001981,UBERON:0002049,UBERON:0002050,UBERON:0002062,UBERON:0002133,UBERON:0002135,UBERON:0002165,UBERON:0002342,UBERON:0002346,UBERON:0002523,UBERON:0002532,UBERON:0003075,UBERON:0003081,UBERON:0003084,UBERON:0003914,UBERON:0003978,UBERON:0004111,UBERON:0004120,UBERON:0004121,UBERON:0004140,UBERON:0004141,UBERON:0004291,UBERON:0004535,UBERON:0004537,UBERON:0004872,UBERON:0004923,UBERON:0005291,UBERON:0005423,UBERON:0005498,UBERON:0005983,UBERON:0006598,UBERON:0006965,UBERON:0007005,UBERON:0007023,UBERON:0007100,UBERON:0007284,UBERON:0007500,UBERON:0007798
|name=heart - mitral valve, adult
|sample_id=10205
|rna_tube_id=103F7
|rna_box=103
|rna_position=F7
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=Biochain
|rna_lot_number=
|rna_catalog_number=R1234131-10
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=
|sample_donor(cell lot)=
|sample_sex=41
|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=0.95
|sample_note=
|profile_hcage=CNhs12855,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=
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|fonse_treatment_closure=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10205-103F7
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010205
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010205
|name=heart - mitral valve, adult
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12855,LSID973,release012,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=103
|rna_catalog_number=R1234131-10
|rna_concentration=0.95
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=F7
|rna_rin=
|rna_sample_type=
|rna_tube_id=103F7
|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=10205
|sample_note=
|sample_sex=41
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=
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}}
}}

Revision as of 14:04, 21 March 2012


Name:heart - mitral valve, 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
sex41
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 numberR1234131-10
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-penis0.526
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-0.347
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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: CNhs12855

Jaspar motifP-value
MA0002.20.00129
MA0003.10.949
MA0004.17.63237e-4
MA0006.10.669
MA0007.10.459
MA0009.10.361
MA0014.10.169
MA0017.10.0784
MA0018.20.0464
MA0019.10.403
MA0024.10.0263
MA0025.10.553
MA0027.10.692
MA0028.16.96262e-7
MA0029.10.628
MA0030.10.944
MA0031.10.808
MA0035.20.332
MA0038.10.025
MA0039.20.0827
MA0040.10.743
MA0041.10.968
MA0042.10.662
MA0043.10.957
MA0046.10.00145
MA0047.20.55
MA0048.10.125
MA0050.10.591
MA0051.10.435
MA0052.18.63038e-23
MA0055.13.69688e-4
MA0057.10.815
MA0058.11.92256e-4
MA0059.11.30363e-4
MA0060.11.15934e-5
MA0061.11.89064e-4
MA0062.26.28282e-13
MA0065.20.0244
MA0066.10.169
MA0067.10.76
MA0068.10.0526
MA0069.10.378
MA0070.10.857
MA0071.10.85
MA0072.10.377
MA0073.10.751
MA0074.10.693
MA0076.17.33996e-9
MA0077.10.782
MA0078.10.321
MA0079.20.62
MA0080.22.65987e-6
MA0081.10.0224
MA0083.13.69059e-4
MA0084.10.955
MA0087.10.753
MA0088.10.00466
MA0090.10.0118
MA0091.10.601
MA0092.10.354
MA0093.14.82154e-4
MA0099.22.39262e-24
MA0100.10.0135
MA0101.10.00177
MA0102.20.188
MA0103.10.00194
MA0104.21.28009e-4
MA0105.11.02052e-6
MA0106.10.00531
MA0107.16.07655e-4
MA0108.26.73359e-14
MA0111.10.889
MA0112.20.383
MA0113.10.194
MA0114.10.0191
MA0115.10.481
MA0116.11.01977e-4
MA0117.10.891
MA0119.10.739
MA0122.10.4
MA0124.10.87
MA0125.10.901
MA0131.10.463
MA0135.10.966
MA0136.11.71777e-12
MA0137.20.131
MA0138.20.405
MA0139.10.0153
MA0140.10.952
MA0141.10.865
MA0142.10.00888
MA0143.10.103
MA0144.10.527
MA0145.10.68
MA0146.10.00886
MA0147.19.22414e-5
MA0148.10.765
MA0149.10.108
MA0150.19.09079e-6
MA0152.10.0723
MA0153.10.385
MA0154.10.0424
MA0155.10.86
MA0156.16.063e-12
MA0157.10.473
MA0159.10.524
MA0160.10.967
MA0162.10.495
MA0163.17.27409e-7
MA0164.10.854
MA0258.10.702
MA0259.10.0434



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: CNhs12855

Novel motifP-value
10.0772
100.117
1000.495
1010.629
1020.266
1030.137
1040.298
1050.573
1060.726
1070.757
1080.364
1090.00472
110.0553
1100.0539
1110.0137
1120.822
1130.724
1140.214
1150.305
1160.75
1170.00873
1180.0352
1190.872
120.818
1200.0573
1210.989
1220.0608
1230.364
1240.202
1250.598
1260.236
1270.274
1280.561
1290.0537
130.054
1300.863
1310.069
1320.151
1330.0421
1340.381
1350.257
1360.105
1370.778
1380.913
1390.693
140.884
1400.849
1410.836
1420.537
1430.00764
1440.436
1450.34
1460.641
1470.0762
1480.433
1490.386
150.16
1500.447
1510.772
1520.506
1530.535
1540.662
1550.646
1560.916
1570.8
1580.36
1590.846
160.276
1600.258
1610.263
1620.703
1630.404
1640.0524
1650.474
1660.0271
1670.0644
1680.794
1690.0646
170.302
180.132
190.353
20.354
200.128
210.344
220.757
230.352
240.105
250.394
260.0571
270.327
280.526
290.00224
30.109
300.28
310.732
320.437
330.0924
340.446
350.605
360.0486
370.135
380.468
390.247
40.215
400.00633
410.245
420.146
430.144
440.999
450.629
460.183
470.0505
480.0403
490.157
50.573
500.877
510.472
520.347
530.709
540.76
550.283
560.393
570.161
580.396
590.543
60.709
600.81
610.0741
620.472
630.554
640.0681
650.722
660.00244
670.571
680.112
690.499
70.16
700.113
710.0151
720.367
730.117
740.113
750.00901
760.346
770.767
780.366
790.224
80.161
800.838
810.439
820.834
830.467
840.778
850.23
860.947
870.00166
880.878
890.859
90.847
900.216
910.175
920.911
930.502
940.0377
950.00197
960.422
970.612
980.428
990.944



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: CNhs12855


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)
0000055 (vessel)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0000946 (cardial valve)
0000948 (heart)
0001009 (circulatory system)
0001048 (primordium)
0001062 (anatomical entity)
0001981 (blood vessel)
0002049 (vasculature)
0002050 (embryonic structure)
0002062 (endocardial cushion)
0002133 (atrioventricular valve)
0002135 (mitral valve)
0002165 (endocardium)
0002342 (neural crest)
0002346 (neurectoderm)
0002523 (tunica intima)
0002532 (epiblast (generic))
0003075 (neural plate)
0003081 (lateral plate mesoderm)
0003084 (heart primordium)
0003914 (epithelial tube)
0003978 (valve)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004872 (splanchnic layer of lateral plate mesoderm)
0004923 (organ component layer)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0005983 (heart layer)
0006598 (presumptive structure)
0006965 (vascular cord)
0007005 (cardiac mesoderm)
0007023 (adult organism)
0007100 (primary circulatory organ)
0007284 (presumptive neural plate)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)

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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