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FF:11584-120F9: 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 17:17, 29 March 2012


Name:Hair Follicle Outer Root Sheath 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 stageNA
sexNA
ageNA
cell typehair follicle, outer root sheath cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC2425
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-0.038
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-0.385
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs12347

Jaspar motifP-value
MA0002.20.484
MA0003.10.208
MA0004.10.695
MA0006.10.507
MA0007.10.111
MA0009.10.22
MA0014.10.808
MA0017.10.135
MA0018.21.49119e-5
MA0019.10.918
MA0024.18.5524e-7
MA0025.12.36407e-4
MA0027.10.626
MA0028.10.2
MA0029.10.208
MA0030.10.324
MA0031.10.643
MA0035.20.187
MA0038.10.0355
MA0039.20.658
MA0040.10.369
MA0041.10.498
MA0042.10.468
MA0043.11.87645e-4
MA0046.10.716
MA0047.20.946
MA0048.10.447
MA0050.10.12
MA0051.10.652
MA0052.10.491
MA0055.10.438
MA0057.10.255
MA0058.10.881
MA0059.10.346
MA0060.12.86184e-8
MA0061.10.612
MA0062.26.07743e-4
MA0065.20.0224
MA0066.10.0415
MA0067.10.0486
MA0068.10.172
MA0069.10.114
MA0070.10.107
MA0071.10.349
MA0072.10.95
MA0073.10.874
MA0074.10.131
MA0076.10.0853
MA0077.10.191
MA0078.10.759
MA0079.20.703
MA0080.21.02574e-5
MA0081.10.125
MA0083.10.224
MA0084.10.365
MA0087.10.425
MA0088.10.176
MA0090.10.00145
MA0091.10.0239
MA0092.10.0801
MA0093.10.603
MA0099.20.218
MA0100.10.371
MA0101.10.188
MA0102.20.35
MA0103.10.0676
MA0104.20.935
MA0105.10.0363
MA0106.10.00824
MA0107.10.133
MA0108.20.778
MA0111.10.986
MA0112.21.20142e-4
MA0113.10.00499
MA0114.10.0647
MA0115.10.0954
MA0116.10.0255
MA0117.10.963
MA0119.10.0246
MA0122.10.989
MA0124.10.343
MA0125.10.115
MA0131.10.155
MA0135.10.923
MA0136.11.17665e-6
MA0137.20.569
MA0138.20.268
MA0139.10.382
MA0140.10.502
MA0141.10.101
MA0142.10.931
MA0143.10.125
MA0144.10.0899
MA0145.10.224
MA0146.10.114
MA0147.10.91
MA0148.10.41
MA0149.10.77
MA0150.10.408
MA0152.10.301
MA0153.10.414
MA0154.10.0865
MA0155.10.299
MA0156.12.30297e-5
MA0157.10.197
MA0159.10.0727
MA0160.10.957
MA0162.10.0946
MA0163.19.92678e-5
MA0164.10.835
MA0258.10.0381
MA0259.10.72



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: CNhs12347

Novel motifP-value
10.122
100.328
1000.558
1010.628
1020.422
1030.0811
1040.455
1050.511
1060.0697
1070.196
1080.225
1090.0287
110.0932
1100.122
1110.493
1120.232
1130.135
1140.0139
1150.737
1160.107
1170.398
1180.45
1190.629
120.52
1200.117
1210.706
1220.228
1230.079
1240.469
1250.166
1260.349
1270.326
1280.0283
1290.89
130.777
1300.897
1310.983
1320.285
1330.441
1340.0876
1350.431
1360.724
1370.15
1380.937
1390.0189
140.951
1400.725
1410.757
1420.144
1430.252
1440.378
1450.178
1460.386
1470.0954
1480.0934
1496.81098e-4
150.628
1500.521
1510.328
1520.198
1530.227
1540.537
1550.303
1560.736
1570.904
1580.0511
1590.206
160.0259
1600.0522
1610.416
1620.224
1630.833
1640.0889
1650.965
1660.724
1670.89
1680.492
1690.0287
170.291
180.137
190.0264
20.398
200.642
210.0205
220.0574
230.234
240.857
250.91
260.0331
270.205
280.172
290.122
30.0669
300.518
310.459
321.39104e-7
330.343
340.965
350.346
360.922
370.014
380.674
390.444
40.218
400.711
410.738
420.575
430.123
440.252
450.786
460.0505
470.206
480.4
490.173
50.489
500.628
510.412
520.42
530.784
540.353
550.00697
560.347
570.406
580.966
590.0512
60.434
600.361
610.826
620.491
630.187
640.473
650.0725
660.278
670.744
680.495
690.0908
70.987
700.042
710.0815
720.543
730.0558
740.279
750.388
760.806
770.028
780.991
790.0147
80.0266
800.353
810.409
820.0649
830.736
840.35
850.0483
860.792
870.0989
880.154
890.0184
90.178
900.961
910.46
920.0185
930.913
940.136
950.131
960.74
970.686
980.597
990.0245



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: CNhs12347


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002371 (somatic cell)
0002559 (hair follicle cell)
0002561 (outer root sheath cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001003 (skin epidermis)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002073 (hair follicle)
0002097 (skin of body)
0002199 (integument)
0002416 (integumental system)
0002532 (epiblast (generic))
0003102 (surface structure)
0004121 (ectoderm-derived structure)
0005086 (hair follicle placode)
0005423 (developing anatomical structure)
0005932 (bulb of hair follicle)
0005933 (hair root sheath)
0005942 (hair outer root sheath)
0007376 (outer epithelium)
0007383 (enveloping layer of ectoderm)

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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