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FF:11271-116H2: 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 17:20, 29 March 2012


Name:Hair Follicle Dermal Papilla Cells, donor1
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 stage28 years old adult
sexmale
age28
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 number1648
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]


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-penis-0.156
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-0.136
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12501

Jaspar motifP-value
MA0002.28.44311e-4
MA0003.10.122
MA0004.10.808
MA0006.10.241
MA0007.10.221
MA0009.10.676
MA0014.10.628
MA0017.10.234
MA0018.20.00757
MA0019.10.493
MA0024.13.19393e-4
MA0025.10.126
MA0027.10.319
MA0028.10.0533
MA0029.10.625
MA0030.10.155
MA0031.10.0678
MA0035.20.168
MA0038.10.489
MA0039.20.379
MA0040.10.799
MA0041.10.432
MA0042.10.7
MA0043.12.23435e-4
MA0046.10.426
MA0047.20.911
MA0048.10.794
MA0050.13.83697e-8
MA0051.11.84274e-6
MA0052.10.664
MA0055.10.864
MA0057.10.465
MA0058.10.637
MA0059.10.368
MA0060.10.22
MA0061.10.0506
MA0062.24.53733e-4
MA0065.20.0264
MA0066.10.105
MA0067.10.174
MA0068.10.347
MA0069.10.513
MA0070.10.931
MA0071.10.769
MA0072.10.672
MA0073.10.466
MA0074.10.351
MA0076.10.0128
MA0077.10.825
MA0078.10.814
MA0079.20.732
MA0080.20.11
MA0081.10.422
MA0083.10.00236
MA0084.10.951
MA0087.10.854
MA0088.10.12
MA0090.10.0468
MA0091.10.0192
MA0092.10.0556
MA0093.10.708
MA0099.24.87114e-5
MA0100.10.453
MA0101.10.0868
MA0102.20.603
MA0103.10.323
MA0104.20.498
MA0105.10.00937
MA0106.10.236
MA0107.10.0356
MA0108.29.74956e-6
MA0111.10.555
MA0112.24.56406e-4
MA0113.10.0631
MA0114.10.118
MA0115.10.84
MA0116.10.02
MA0117.10.992
MA0119.10.0775
MA0122.10.608
MA0124.10.739
MA0125.10.458
MA0131.10.109
MA0135.10.414
MA0136.10.0998
MA0137.20.904
MA0138.20.19
MA0139.10.353
MA0140.10.441
MA0141.10.515
MA0142.10.0276
MA0143.10.532
MA0144.10.248
MA0145.10.176
MA0146.10.144
MA0147.10.606
MA0148.10.51
MA0149.10.0902
MA0150.10.126
MA0152.10.075
MA0153.10.385
MA0154.10.0147
MA0155.10.136
MA0156.10.434
MA0157.10.792
MA0159.10.255
MA0160.10.578
MA0162.10.0298
MA0163.10.00293
MA0164.10.801
MA0258.10.0124
MA0259.10.314



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: CNhs12501

Novel motifP-value
10.315
100.828
1000.879
1010.895
1020.354
1030.0962
1040.365
1050.559
1060.00476
1070.0298
1080.791
1090.0926
110.0802
1100.205
1110.699
1120.133
1130.359
1140.115
1150.436
1160.0911
1170.451
1180.864
1190.284
120.874
1200.332
1210.426
1220.477
1230.222
1240.269
1250.957
1260.285
1270.0434
1280.00555
1290.38
130.521
1300.0774
1310.697
1320.82
1330.548
1340.137
1350.0279
1360.355
1370.477
1380.767
1390.436
140.86
1400.991
1410.397
1420.0574
1430.0305
1440.519
1450.162
1460.156
1470.362
1480.471
1490.0357
150.48
1500.173
1510.582
1520.0948
1530.803
1540.668
1550.265
1560.823
1570.642
1580.342
1590.451
160.182
1600.0961
1610.653
1620.294
1630.929
1640.851
1650.437
1660.321
1670.962
1680.257
1690.0227
170.151
180.0795
190.0224
20.165
200.464
210.461
220.138
230.117
240.44
250.964
260.0214
270.241
280.942
290.277
30.461
300.155
310.836
325.48849e-5
330.621
340.304
350.516
360.86
370.0669
380.543
390.75
40.725
400.565
410.144
420.607
430.12
440.484
450.165
460.071
470.295
480.307
490.251
50.452
500.529
510.646
520.169
530.795
540.716
550.531
560.287
570.288
580.534
590.0362
60.666
600.0932
610.686
620.203
630.178
640.309
650.0666
660.757
670.688
680.0793
690.938
70.678
700.0527
710.112
720.347
730.0991
740.536
750.497
760.819
770.0441
780.904
790.0234
80.103
800.251
810.666
820.412
830.0972
840.533
850.0368
860.365
870.139
880.457
890.061
90.0911
900.129
910.701
920.202
930.93
940.189
950.378
960.477
970.52
980.246
990.225



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: CNhs12501


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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