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{{f5samples
{{f5samples
|id=FF:11348-117G7
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000119,UBERON:0000412,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000486,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000926,UBERON:0001003,UBERON:0001048,UBERON:0001062,UBERON:0001992,UBERON:0002050,UBERON:0002067,UBERON:0002073,UBERON:0002097,UBERON:0002199,UBERON:0002329,UBERON:0002384,UBERON:0002416,UBERON:0002532,UBERON:0003059,UBERON:0003077,UBERON:0003102,UBERON:0003104,UBERON:0004016,UBERON:0004120,UBERON:0004121,UBERON:0004290,UBERON:0004923,UBERON:0005086,UBERON:0005291,UBERON:0005423,UBERON:0007376,UBERON:0007383,UBERON:0009142
|name=Hair Follicle Dermal Papilla Cells, donor2
|sample_id=11348
|rna_tube_id=117G7
|rna_box=117
|rna_position=G7
|sample_cell_lot=N/A
|sample_cell_catalog=N/A
|sample_company=Cell Applications
|rna_lot_number=1866
|rna_catalog_number=CA602-R10a
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=51 years old adult
|sample_tissue=hair follicle
|sample_donor(cell lot)=
|sample_sex=female
|sample_age=51
|sample_ethnicity=C
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=hair follicle, dermal papilla cell
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_weight_ug=10
|rna_concentration=0.5
|sample_note=
|profile_hcage=CNhs11979,LSID836,release011,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=SRhi10007,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000133,CL:0000134,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000255,CL:0000333,CL:0000346,CL:0000548,CL:0000723,CL:0002320,CL:0002321,CL:0002371,CL:0002559
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000133,CL:0000134,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000255,CL:0000333,CL:0000346,CL:0000548,CL:0000723,CL:0002320,CL:0002321,CL:0002371,CL:0002559
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000119,UBERON:0000412,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000486,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000926,UBERON:0001003,UBERON:0001048,UBERON:0001062,UBERON:0001992,UBERON:0002050,UBERON:0002067,UBERON:0002073,UBERON:0002097,UBERON:0002199,UBERON:0002329,UBERON:0002384,UBERON:0002416,UBERON:0002532,UBERON:0003059,UBERON:0003077,UBERON:0003102,UBERON:0003104,UBERON:0004016,UBERON:0004120,UBERON:0004121,UBERON:0004290,UBERON:0004923,UBERON:0005086,UBERON:0005291,UBERON:0005423,UBERON:0007376,UBERON:0007383,UBERON:0009142
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
|created_by=
|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:11348-117G7
|is_a=EFO:0002091;;FF:0000002;;FF:0000071;;FF:0000210
|is_a=EFO:0002091;;FF:0000002;;FF:0000071;;FF:0000210
|name=Hair Follicle Dermal Papilla Cells, donor2
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11979,LSID836,release011,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=SRhi10007,,,
|rna_box=117
|rna_catalog_number=CA602-R10a
|rna_concentration=0.5
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_lot_number=1866
|rna_od260/230=
|rna_od260/280=
|rna_position=G7
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=117G7
|rna_weight_ug=10
|sample_age=51
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_lot=N/A
|sample_cell_type=hair follicle, dermal papilla cell
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Cell Applications
|sample_description=
|sample_dev_stage=51 years old adult
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=11348
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=hair follicle
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}}
}}

Revision as of 14:52, 21 March 2012


Name:Hair Follicle Dermal Papilla Cells, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuehair follicle
dev stage51 years old adult
sexfemale
age51
cell typehair follicle, dermal papilla cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1866
catalog numberCA602-R10a
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]





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
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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
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: CNhs11979

Jaspar motifP-value
MA0002.20.643
MA0003.10.169
MA0004.10.334
MA0006.10.0928
MA0007.10.549
MA0009.10.406
MA0014.10.407
MA0017.10.803
MA0018.22.17428e-5
MA0019.10.437
MA0024.13.65497e-5
MA0025.10.00904
MA0027.10.592
MA0028.10.00181
MA0029.10.629
MA0030.10.0103
MA0031.10.00759
MA0035.20.0211
MA0038.10.0162
MA0039.20.268
MA0040.10.931
MA0041.10.493
MA0042.10.732
MA0043.11.43037e-7
MA0046.10.593
MA0047.20.346
MA0048.10.213
MA0050.10.0188
MA0051.10.0282
MA0052.10.0932
MA0055.10.834
MA0057.10.0978
MA0058.10.186
MA0059.10.989
MA0060.11.24962e-4
MA0061.10.913
MA0062.24.71329e-8
MA0065.20.593
MA0066.10.504
MA0067.10.00747
MA0068.10.687
MA0069.10.233
MA0070.10.689
MA0071.10.927
MA0072.10.485
MA0073.10.645
MA0074.10.173
MA0076.12.30744e-4
MA0077.10.344
MA0078.10.652
MA0079.20.469
MA0080.28.54422e-7
MA0081.10.00399
MA0083.10.0486
MA0084.10.276
MA0087.10.952
MA0088.10.732
MA0090.10.0714
MA0091.10.0402
MA0092.10.298
MA0093.10.249
MA0099.22.83081e-4
MA0100.10.145
MA0101.10.135
MA0102.20.134
MA0103.10.325
MA0104.20.0308
MA0105.10.396
MA0106.10.208
MA0107.10.217
MA0108.20.204
MA0111.10.703
MA0112.20.00375
MA0113.10.547
MA0114.10.548
MA0115.10.231
MA0116.10.104
MA0117.10.175
MA0119.10.495
MA0122.10.161
MA0124.10.132
MA0125.10.126
MA0131.10.0686
MA0135.10.856
MA0136.17.14642e-10
MA0137.20.195
MA0138.20.12
MA0139.10.629
MA0140.10.0142
MA0141.10.506
MA0142.10.977
MA0143.10.658
MA0144.10.767
MA0145.10.22
MA0146.10.287
MA0147.10.0465
MA0148.10.404
MA0149.10.743
MA0150.10.00889
MA0152.10.0552
MA0153.10.237
MA0154.10.0775
MA0155.10.0274
MA0156.18.73722e-8
MA0157.10.0939
MA0159.10.735
MA0160.10.254
MA0162.10.0362
MA0163.10.0622
MA0164.10.969
MA0258.10.107
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: CNhs11979

Novel motifP-value
10.894
100.784
1000.909
1010.34
1020.496
1030.397
1040.665
1050.535
1060.0204
1070.00792
1080.36
1090.178
110.247
1100.281
1110.602
1120.393
1130.0062
1140.379
1150.0182
1160.0295
1170.709
1180.793
1190.732
120.473
1200.196
1210.938
1220.0326
1230.0128
1240.685
1250.833
1260.969
1270.945
1280.0195
1290.63
130.875
1300.332
1310.592
1320.146
1330.45
1340.795
1350.897
1360.565
1370.221
1380.609
1390.984
140.349
1400.447
1410.322
1420.286
1430.65
1440.505
1450.278
1460.975
1470.0501
1480.688
1490.0161
150.44
1500.21
1510.743
1520.0321
1530.62
1540.66
1550.163
1560.778
1570.476
1580.0153
1590.657
160.0925
1600.364
1610.651
1620.195
1630.713
1640.552
1650.186
1660.677
1670.0706
1680.891
1690.0617
170.284
180.447
190.0053
20.134
200.713
210.219
220.183
230.19
240.83
250.418
260.0598
270.332
280.278
290.642
30.775
300.159
310.64
321.0765e-10
330.813
340.484
350.981
360.0116
370.162
380.825
390.281
40.488
400.437
410.651
420.532
430.325
440.095
450.395
460.137
470.808
480.535
490.97
50.713
500.49
510.494
520.341
530.396
540.527
550.428
560.677
570.935
580.588
590.0116
60.903
600.373
610.232
620.568
630.368
640.816
650.35
660.27
670.77
680.521
690.575
70.348
700.359
710.558
720.797
730.0262
740.856
750.93
760.735
770.00352
780.918
792.95825e-4
80.171
800.184
810.944
820.0882
830.00511
840.579
850.00802
860.567
870.0745
880.467
890.0453
90.307
900.558
910.872
920.53
930.448
940.612
950.495
960.88
970.972
980.972
990.00571



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: CNhs11979


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000133 (neurectodermal cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000333 (migratory neural crest cell)
0000346 (hair follicle dermal papilla cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002559 (hair follicle cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000412 (dermal papilla)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0001003 (skin epidermis)
0001048 (primordium)
0001062 (anatomical entity)
0001992 (papillary layer of dermis)
0002050 (embryonic structure)
0002067 (dermis)
0002073 (hair follicle)
0002097 (skin of body)
0002199 (integument)
0002329 (somite)
0002384 (connective tissue)
0002416 (integumental system)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003102 (surface structure)
0003104 (mesenchyme)
0004016 (dermatome)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004290 (dermomyotome)
0004923 (organ component layer)
0005086 (hair follicle placode)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0007376 (outer epithelium)
0007383 (enveloping layer of ectoderm)
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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