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FF:11269-116G9: 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:Fibroblast - Dermal, donor1
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 stage71 years old adult
sexmale
age71
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 number1378
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-penis0.0654
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-0.0954
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs12499

Jaspar motifP-value
MA0002.20.794
MA0003.10.199
MA0004.10.117
MA0006.10.965
MA0007.10.028
MA0009.10.289
MA0014.10.998
MA0017.10.407
MA0018.25.54934e-7
MA0019.10.748
MA0024.11.16689e-4
MA0025.10.00332
MA0027.10.864
MA0028.10.59
MA0029.10.308
MA0030.10.0679
MA0031.10.22
MA0035.20.188
MA0038.13.71776e-4
MA0039.20.23
MA0040.10.854
MA0041.10.559
MA0042.10.722
MA0043.11.16004e-7
MA0046.10.602
MA0047.20.219
MA0048.10.352
MA0050.19.94855e-6
MA0051.10.0088
MA0052.10.931
MA0055.10.4
MA0057.10.179
MA0058.10.131
MA0059.10.0108
MA0060.16.40247e-7
MA0061.10.535
MA0062.20.00315
MA0065.20.0861
MA0066.10.0286
MA0067.10.0177
MA0068.10.16
MA0069.10.374
MA0070.10.937
MA0071.10.282
MA0072.10.949
MA0073.10.768
MA0074.10.202
MA0076.10.138
MA0077.10.525
MA0078.10.613
MA0079.20.971
MA0080.23.64887e-5
MA0081.10.132
MA0083.10.434
MA0084.10.704
MA0087.10.636
MA0088.10.00295
MA0090.10.0765
MA0091.10.112
MA0092.10.597
MA0093.10.177
MA0099.22.04336e-4
MA0100.10.949
MA0101.10.0178
MA0102.20.0827
MA0103.10.0956
MA0104.20.0225
MA0105.10.138
MA0106.10.0133
MA0107.10.00517
MA0108.20.625
MA0111.10.926
MA0112.20.00318
MA0113.10.0918
MA0114.10.206
MA0115.10.878
MA0116.10.121
MA0117.10.164
MA0119.10.0759
MA0122.10.675
MA0124.10.351
MA0125.10.169
MA0131.10.0652
MA0135.10.384
MA0136.19.36107e-5
MA0137.20.124
MA0138.20.612
MA0139.10.618
MA0140.10.295
MA0141.10.00915
MA0142.10.336
MA0143.10.36
MA0144.10.984
MA0145.10.529
MA0146.10.215
MA0147.10.0109
MA0148.10.288
MA0149.10.178
MA0150.10.974
MA0152.10.312
MA0153.10.86
MA0154.10.376
MA0155.10.629
MA0156.12.2634e-4
MA0157.10.703
MA0159.10.223
MA0160.10.389
MA0162.10.115
MA0163.16.66194e-4
MA0164.10.598
MA0258.10.202
MA0259.10.178



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: CNhs12499

Novel motifP-value
10.224
100.162
1000.607
1010.782
1020.732
1030.0788
1040.573
1050.394
1060.458
1070.61
1080.0945
1090.0362
110.0664
1100.0627
1110.0696
1120.392
1130.0248
1140.083
1150.428
1160.0394
1170.245
1180.218
1190.946
120.663
1200.0172
1210.808
1220.301
1230.0142
1240.559
1250.515
1260.544
1270.413
1280.286
1290.748
130.616
1300.696
1310.911
1320.436
1330.387
1340.154
1350.762
1360.651
1370.183
1380.81
1390.827
140.235
1400.771
1410.704
1420.937
1430.063
1440.386
1450.297
1460.495
1470.0594
1480.48
1490.0539
150.444
1500.347
1510.587
1520.102
1530.386
1540.52
1550.0632
1560.327
1570.986
1580.0683
1590.286
160.0629
1600.0666
1610.614
1620.579
1630.883
1640.112
1650.821
1660.641
1670.853
1680.13
1690.0149
170.215
180.0566
190.0258
20.488
200.855
210.0709
220.074
230.586
240.373
250.693
260.059
270.116
280.146
290.0604
30.342
300.677
310.514
320.00862
330.426
340.872
350.459
360.324
370.0357
380.818
390.244
40.108
400.623
410.709
420.907
430.153
440.118
450.853
460.0749
470.365
480.234
490.308
50.847
500.313
510.172
520.883
530.252
540.251
550.079
560.804
570.297
580.768
590.156
60.888
600.969
610.76
620.685
630.0898
640.649
650.251
660.711
670.705
680.473
690.222
70.547
700.0461
710.115
720.826
730.0247
740.323
750.135
760.63
770.0711
780.78
790.114
80.00768
800.265
810.589
820.467
830.884
840.134
850.0785
860.72
870.0234
880.732
890.0635
90.252
900.993
910.985
920.0799
930.87
940.209
950.0672
960.874
970.85
980.398
990.011



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: CNhs12499


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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