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FF:11418-118F5: 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:Fibroblast - Dermal, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
dev stage41 years old adult
sexfemale
age41
cell typefibroblast
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1375
catalog numberCA106-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-penis0.27
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-0.104
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs12028

Jaspar motifP-value
MA0002.20.738
MA0003.10.356
MA0004.10.51
MA0006.10.8
MA0007.10.0309
MA0009.10.224
MA0014.10.922
MA0017.10.402
MA0018.22.49176e-6
MA0019.10.708
MA0024.10.00138
MA0025.17.52601e-5
MA0027.10.659
MA0028.10.0259
MA0029.10.71
MA0030.10.0171
MA0031.10.163
MA0035.20.0891
MA0038.11.89264e-4
MA0039.20.0778
MA0040.10.549
MA0041.10.732
MA0042.10.399
MA0043.12.58939e-8
MA0046.10.229
MA0047.20.577
MA0048.10.0386
MA0050.15.95606e-4
MA0051.10.0435
MA0052.10.466
MA0055.10.324
MA0057.10.296
MA0058.10.542
MA0059.10.0386
MA0060.14.74086e-9
MA0061.10.813
MA0062.27.153e-8
MA0065.20.179
MA0066.10.0516
MA0067.10.0252
MA0068.10.0292
MA0069.10.488
MA0070.10.707
MA0071.10.174
MA0072.10.604
MA0073.10.644
MA0074.10.172
MA0076.17.57305e-4
MA0077.10.287
MA0078.10.94
MA0079.20.566
MA0080.24.05485e-7
MA0081.10.0238
MA0083.10.253
MA0084.10.422
MA0087.10.489
MA0088.10.106
MA0090.10.177
MA0091.10.216
MA0092.10.424
MA0093.10.62
MA0099.20.913
MA0100.10.511
MA0101.10.0168
MA0102.20.103
MA0103.10.187
MA0104.20.232
MA0105.10.0884
MA0106.10.0138
MA0107.10.0204
MA0108.20.312
MA0111.10.63
MA0112.20.00728
MA0113.10.126
MA0114.10.443
MA0115.10.892
MA0116.10.151
MA0117.10.305
MA0119.10.0325
MA0122.10.284
MA0124.10.917
MA0125.10.0369
MA0131.10.314
MA0135.10.688
MA0136.11.8344e-8
MA0137.20.0843
MA0138.20.376
MA0139.10.851
MA0140.10.179
MA0141.10.0248
MA0142.10.881
MA0143.10.412
MA0144.10.808
MA0145.10.789
MA0146.10.179
MA0147.10.129
MA0148.10.75
MA0149.10.206
MA0150.10.33
MA0152.10.273
MA0153.10.364
MA0154.10.548
MA0155.10.576
MA0156.11.57815e-8
MA0157.10.342
MA0159.10.665
MA0160.10.632
MA0162.10.258
MA0163.10.00134
MA0164.10.797
MA0258.10.0963
MA0259.10.652



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: CNhs12028

Novel motifP-value
10.198
100.0474
1000.312
1010.911
1020.686
1030.495
1040.625
1050.0953
1060.044
1070.0637
1080.0985
1090.101
110.177
1100.101
1110.0512
1120.206
1130.015
1140.0762
1150.0801
1160.0453
1170.207
1180.259
1190.518
120.443
1200.0775
1210.519
1220.0431
1230.158
1240.499
1250.174
1260.651
1270.609
1280.0456
1290.565
130.575
1300.665
1310.607
1320.298
1330.381
1340.4
1350.385
1360.931
1370.227
1380.899
1390.518
140.145
1400.382
1410.684
1420.388
1430.195
1440.708
1450.0582
1460.711
1470.0555
1480.0394
1490.241
150.687
1500.137
1510.439
1520.0166
1530.269
1540.667
1550.234
1560.268
1570.745
1580.13
1590.491
160.0401
1600.032
1610.627
1620.538
1630.955
1640.0233
1650.678
1660.842
1670.45
1680.599
1690.023
170.291
180.0858
190.0312
20.587
200.667
210.00775
220.185
230.666
240.794
250.457
260.0995
270.235
280.179
290.119
30.242
300.987
310.608
322.18237e-5
330.397
340.806
350.628
360.233
370.0182
380.909
390.236
40.396
400.569
410.366
420.944
430.2
440.0218
450.754
460.0993
470.702
480.445
490.246
50.877
500.41
510.522
520.675
530.314
540.626
550.195
560.621
570.359
580.631
590.189
60.969
600.611
610.876
620.75
630.17
640.769
650.359
660.441
670.573
680.255
690.245
70.431
700.0969
710.129
720.537
730.00919
740.0176
750.115
760.602
770.0869
780.892
790.0345
80.00562
800.0212
810.422
820.732
830.191
840.425
850.135
860.942
870.139
880.245
890.303
90.421
900.598
910.365
920.107
930.995
940.315
950.0266
960.284
970.639
980.318
990.0151



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: CNhs12028


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)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002551 (fibroblast of dermis)
0002620 (skin fibroblast)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
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)
0000926 (mesoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002067 (dermis)
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)
0004290 (dermomyotome)
0004923 (organ component layer)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
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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