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FF:11346-117G5: 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 16:47, 29 March 2012


Name:Fibroblast - Dermal, donor2
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 stage68 years old adult
sexfemale
age68
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 number1616
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-penis0.21
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-lymphoma0.161
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
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs11379

Jaspar motifP-value
MA0002.20.323
MA0003.10.429
MA0004.10.195
MA0006.10.786
MA0007.10.00167
MA0009.10.749
MA0014.10.499
MA0017.10.345
MA0018.23.3869e-4
MA0019.10.796
MA0024.10.189
MA0025.10.165
MA0027.10.538
MA0028.10.272
MA0029.10.525
MA0030.10.177
MA0031.10.515
MA0035.20.299
MA0038.10.107
MA0039.20.133
MA0040.10.69
MA0041.10.508
MA0042.10.914
MA0043.11.50085e-4
MA0046.10.981
MA0047.20.168
MA0048.10.245
MA0050.11.50734e-6
MA0051.10.0425
MA0052.10.153
MA0055.10.00202
MA0057.10.0551
MA0058.10.224
MA0059.10.00345
MA0060.10.0112
MA0061.10.567
MA0062.20.754
MA0065.20.315
MA0066.10.161
MA0067.10.0202
MA0068.10.33
MA0069.10.217
MA0070.10.247
MA0071.10.476
MA0072.10.428
MA0073.10.998
MA0074.10.657
MA0076.10.958
MA0077.10.674
MA0078.10.966
MA0079.20.536
MA0080.20.304
MA0081.10.376
MA0083.10.0801
MA0084.10.769
MA0087.10.624
MA0088.10.01
MA0090.10.0818
MA0091.10.229
MA0092.10.361
MA0093.10.264
MA0099.21.71152e-17
MA0100.10.902
MA0101.10.49
MA0102.20.0305
MA0103.10.18
MA0104.20.0903
MA0105.10.367
MA0106.10.00524
MA0107.10.172
MA0108.25.48841e-5
MA0111.10.533
MA0112.20.0135
MA0113.10.00297
MA0114.10.229
MA0115.10.712
MA0116.10.284
MA0117.10.292
MA0119.10.00951
MA0122.10.899
MA0124.10.164
MA0125.10.654
MA0131.10.887
MA0135.10.326
MA0136.10.234
MA0137.20.0723
MA0138.20.979
MA0139.10.488
MA0140.10.0838
MA0141.10.0264
MA0142.10.209
MA0143.10.151
MA0144.10.553
MA0145.10.183
MA0146.10.452
MA0147.10.0181
MA0148.10.51
MA0149.10.00746
MA0150.10.00756
MA0152.10.575
MA0153.10.773
MA0154.10.437
MA0155.10.264
MA0156.10.301
MA0157.10.98
MA0159.10.319
MA0160.10.205
MA0162.10.101
MA0163.10.0275
MA0164.10.713
MA0258.10.327
MA0259.10.0724



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: CNhs11379

Novel motifP-value
10.122
100.453
1000.369
1010.646
1020.272
1030.966
1040.315
1050.224
1060.656
1070.298
1080.36
1090.00222
110.0457
1100.0165
1110.604
1120.882
1130.343
1140.133
1150.725
1160.55
1170.525
1180.885
1190.352
120.78
1200.103
1210.308
1220.483
1230.0973
1240.649
1250.574
1260.898
1270.177
1280.382
1290.86
130.104
1300.0711
1310.755
1320.903
1330.188
1340.425
1350.671
1360.308
1370.178
1380.762
1390.943
140.402
1400.508
1410.715
1420.89
1430.0418
1440.517
1450.0277
1460.0337
1470.0835
1480.507
1490.179
150.322
1500.279
1510.658
1520.158
1530.479
1540.559
1550.126
1560.369
1570.43
1580.204
1590.488
160.799
1600.00282
1610.777
1620.961
1630.985
1640.827
1650.646
1660.736
1670.431
1680.472
1690.0518
170.191
180.0744
190.114
20.78
200.905
210.444
220.21
230.479
240.134
250.66
260.0888
270.288
280.133
290.682
30.485
300.611
310.882
320.817
330.0186
340.375
350.813
360.143
370.193
380.42
390.554
40.636
400.0469
410.586
420.355
430.232
440.407
450.688
460.0965
470.217
480.0493
490.273
50.758
500.329
510.647
520.646
530.784
540.721
550.836
560.503
570.0382
580.958
590.604
60.664
600.872
610.781
620.613
630.112
640.315
650.29
660.0156
670.735
680.0919
690.182
70.541
700.402
710.0177
720.97
730.0134
740.722
750.28
760.928
770.122
780.991
790.356
80.00344
800.579
810.611
820.74
830.551
840.0856
850.584
860.629
870.0439
880.197
890.0963
90.14
900.0715
910.731
920.799
930.328
940.525
950.0265
960.219
970.302
980.0329
999.36232e-4



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: CNhs11379


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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