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FF:11504-119G1: 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 17:16, 29 March 2012


Name:Hair Follicle Outer Root Sheath 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 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-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-penis0.129
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-0.393
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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: CNhs12339

Jaspar motifP-value
MA0002.20.238
MA0003.10.372
MA0004.10.273
MA0006.10.489
MA0007.10.0451
MA0009.10.384
MA0014.10.794
MA0017.10.813
MA0018.20.0019
MA0019.10.528
MA0024.11.37605e-8
MA0025.10.00141
MA0027.10.568
MA0028.10.846
MA0029.10.89
MA0030.10.698
MA0031.10.454
MA0035.20.00659
MA0038.10.0116
MA0039.20.0884
MA0040.10.513
MA0041.10.765
MA0042.10.795
MA0043.10.0119
MA0046.10.264
MA0047.20.997
MA0048.10.0896
MA0050.10.968
MA0051.10.768
MA0052.10.754
MA0055.10.575
MA0057.10.855
MA0058.10.283
MA0059.10.692
MA0060.11.60152e-11
MA0061.10.798
MA0062.20.00237
MA0065.20.553
MA0066.10.394
MA0067.10.0546
MA0068.10.984
MA0069.10.129
MA0070.10.302
MA0071.10.917
MA0072.10.631
MA0073.10.824
MA0074.10.0464
MA0076.10.4
MA0077.10.103
MA0078.10.374
MA0079.20.109
MA0080.22.41241e-7
MA0081.10.049
MA0083.11.04269e-4
MA0084.10.017
MA0087.10.197
MA0088.10.369
MA0090.10.00164
MA0091.10.0959
MA0092.10.0984
MA0093.10.204
MA0099.22.23728e-4
MA0100.10.528
MA0101.10.0848
MA0102.20.885
MA0103.11.63034e-4
MA0104.20.396
MA0105.10.0334
MA0106.10.0854
MA0107.10.094
MA0108.20.109
MA0111.10.855
MA0112.20.00254
MA0113.10.0058
MA0114.10.308
MA0115.10.0538
MA0116.10.0605
MA0117.10.845
MA0119.10.00894
MA0122.10.652
MA0124.10.277
MA0125.10.423
MA0131.10.611
MA0135.10.318
MA0136.11.39435e-6
MA0137.20.366
MA0138.20.578
MA0139.10.825
MA0140.10.0824
MA0141.10.989
MA0142.10.704
MA0143.10.128
MA0144.10.043
MA0145.10.365
MA0146.10.168
MA0147.10.426
MA0148.10.839
MA0149.10.465
MA0150.10.00674
MA0152.10.0804
MA0153.10.74
MA0154.10.122
MA0155.10.677
MA0156.14.17065e-6
MA0157.10.0884
MA0159.10.511
MA0160.10.13
MA0162.10.104
MA0163.11.76246e-4
MA0164.10.624
MA0258.10.369
MA0259.10.424



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: CNhs12339

Novel motifP-value
10.695
100.059
1000.62
1010.723
1020.0474
1030.0941
1040.404
1050.35
1060.119
1070.202
1080.31
1090.237
110.893
1100.404
1110.777
1120.363
1130.164
1140.0739
1150.853
1160.0337
1170.202
1180.927
1190.79
120.337
1200.199
1210.448
1220.00301
1230.00275
1240.617
1250.988
1260.699
1270.841
1280.112
1290.37
130.994
1300.853
1310.86
1320.23
1330.897
1340.581
1350.848
1360.396
1370.109
1380.972
1390.514
140.377
1400.426
1410.508
1420.859
1430.882
1440.226
1450.324
1460.969
1470.259
1480.395
1490.0342
150.473
1500.473
1510.678
1520.157
1530.115
1540.358
1550.14
1560.318
1570.727
1580.116
1590.652
160.0358
1600.122
1610.538
1620.357
1630.396
1640.0441
1650.916
1660.537
1670.862
1680.801
1690.0363
170.492
180.343
190.0139
20.703
200.747
210.166
220.156
230.385
240.975
250.369
260.0165
270.551
280.238
290.0538
30.0454
300.796
310.947
328.45585e-8
330.272
340.438
350.522
360.66
370.0153
380.658
390.484
40.0376
400.477
410.564
420.663
430.474
440.734
450.49
460.0901
470.994
480.768
490.643
50.819
500.592
510.805
520.82
530.155
540.77
553.31546e-4
560.62
570.868
580.435
590.199
60.829
600.77
610.639
620.813
630.335
640.332
650.369
660.263
670.613
680.467
690.454
70.26
700.114
710.0742
720.872
730.0154
740.35
750.19
760.432
770.157
780.829
790.0464
80.238
800.139
810.939
820.651
830.525
840.111
850.0661
860.838
870.733
880.106
890.155
90.599
900.363
910.806
920.0373
930.146
940.458
950.126
960.951
970.991
980.58
990.00193



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: CNhs12339


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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