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FF:11420-118F7: 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 17:07, 29 March 2012


Name:Hair Follicle Dermal Papilla Cells, donor3
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 stage36 years old adult
sexfemale
age36
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 number1388
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-0.159
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-lymphoma0.0419
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: CNhs12030

Jaspar motifP-value
MA0002.25.68674e-4
MA0003.10.125
MA0004.10.991
MA0006.10.167
MA0007.10.067
MA0009.10.627
MA0014.10.97
MA0017.10.754
MA0018.20.029
MA0019.10.187
MA0024.10.467
MA0025.10.229
MA0027.10.886
MA0028.10.0541
MA0029.10.791
MA0030.10.255
MA0031.10.00157
MA0035.20.898
MA0038.10.571
MA0039.20.478
MA0040.10.964
MA0041.10.312
MA0042.10.47
MA0043.12.97726e-6
MA0046.10.0146
MA0047.20.592
MA0048.10.288
MA0050.10.273
MA0051.10.573
MA0052.10.00646
MA0055.10.0627
MA0057.10.12
MA0058.10.62
MA0059.10.315
MA0060.10.0104
MA0061.10.545
MA0062.20.00435
MA0065.20.111
MA0066.10.43
MA0067.10.122
MA0068.10.157
MA0069.10.51
MA0070.10.195
MA0071.10.695
MA0072.10.816
MA0073.10.615
MA0074.10.402
MA0076.10.006
MA0077.10.489
MA0078.10.96
MA0079.20.797
MA0080.20.107
MA0081.10.51
MA0083.10.00273
MA0084.10.733
MA0087.10.638
MA0088.10.114
MA0090.10.00922
MA0091.10.0594
MA0092.10.046
MA0093.10.845
MA0099.22.11266e-14
MA0100.10.434
MA0101.10.852
MA0102.20.00215
MA0103.10.184
MA0104.20.652
MA0105.10.245
MA0106.10.0877
MA0107.10.886
MA0108.23.6015e-5
MA0111.10.386
MA0112.20.00455
MA0113.10.285
MA0114.10.351
MA0115.10.508
MA0116.10.122
MA0117.10.506
MA0119.10.141
MA0122.10.681
MA0124.10.901
MA0125.10.973
MA0131.10.172
MA0135.10.0288
MA0136.10.146
MA0137.20.237
MA0138.20.066
MA0139.10.901
MA0140.10.923
MA0141.10.106
MA0142.10.163
MA0143.10.431
MA0144.10.936
MA0145.10.154
MA0146.10.0642
MA0147.10.985
MA0148.10.614
MA0149.10.137
MA0150.10.00625
MA0152.10.531
MA0153.10.144
MA0154.10.0813
MA0155.10.133
MA0156.10.262
MA0157.10.164
MA0159.10.671
MA0160.10.071
MA0162.10.0475
MA0163.10.0474
MA0164.10.547
MA0258.10.027
MA0259.10.668



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: CNhs12030

Novel motifP-value
10.765
100.857
1000.933
1010.227
1020.827
1030.807
1040.544
1050.105
1060.0292
1070.0129
1080.909
1090.0284
110.0803
1100.166
1110.624
1120.671
1130.183
1140.333
1150.856
1160.149
1170.476
1180.898
1190.156
120.161
1200.264
1210.375
1220.44
1230.411
1240.481
1250.868
1260.438
1270.108
1280.191
1290.706
130.788
1300.00998
1310.979
1320.939
1330.785
1340.73
1350.161
1360.509
1370.493
1380.815
1390.522
140.575
1400.975
1410.663
1420.00706
1430.0255
1440.891
1450.179
1460.0444
1470.244
1480.34
1490.202
150.567
1500.195
1510.55
1520.0431
1530.354
1540.64
1550.322
1560.322
1570.998
1580.0975
1590.506
160.209
1600.0563
1610.635
1620.0209
1630.467
1640.622
1650.222
1660.138
1670.487
1680.774
1690.0371
170.147
180.262
190.0554
20.277
200.287
210.738
220.0824
230.201
240.179
250.597
260.00315
270.293
280.263
290.767
30.634
300.168
310.511
320.0124
330.25
340.29
350.854
360.831
370.227
380.643
390.56
40.686
400.0493
410.693
420.752
430.132
440.476
450.237
460.0617
470.501
480.167
490.263
50.863
500.365
510.452
520.205
530.962
540.659
550.672
560.511
570.339
580.959
590.0246
60.988
600.332
610.425
620.59
630.217
640.313
650.167
660.279
670.753
680.403
690.106
70.851
700.876
710.112
720.955
730.0377
740.743
750.863
760.55
770.0116
780.652
790.442
80.0833
800.799
810.675
820.496
830.448
840.203
850.119
860.842
870.0324
880.191
890.515
90.0963
900.132
910.0487
920.887
930.784
940.387
950.122
960.348
970.412
980.131
990.0109



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: CNhs12030


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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