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FF:11245-116E3: 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 16:36, 29 March 2012


Name:Fibroblast - Aortic Adventitial, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueaorta
dev stage68 years old adult
sexfemale
age68
cell typefibroblast
cell lineNA
companyLonza
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-0.0308
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-lymphoma0.245
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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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: CNhs10874

Jaspar motifP-value
MA0002.20.123
MA0003.10.955
MA0004.10.0686
MA0006.10.0704
MA0007.10.797
MA0009.10.286
MA0014.10.452
MA0017.10.151
MA0018.26.68389e-7
MA0019.10.456
MA0024.10.926
MA0025.10.0426
MA0027.10.705
MA0028.10.886
MA0029.10.318
MA0030.10.0933
MA0031.10.074
MA0035.20.388
MA0038.10.224
MA0039.20.039
MA0040.10.806
MA0041.10.665
MA0042.10.913
MA0043.11.40105e-4
MA0046.10.0816
MA0047.20.363
MA0048.10.0257
MA0050.10.00607
MA0051.10.214
MA0052.10.312
MA0055.10.447
MA0057.10.327
MA0058.10.0238
MA0059.10.76
MA0060.10.0647
MA0061.10.0304
MA0062.23.90044e-4
MA0065.20.303
MA0066.10.45
MA0067.18.83091e-4
MA0068.10.72
MA0069.10.222
MA0070.10.937
MA0071.10.342
MA0072.10.257
MA0073.10.799
MA0074.10.897
MA0076.10.297
MA0077.10.63
MA0078.10.797
MA0079.20.669
MA0080.25.43151e-8
MA0081.10.0342
MA0083.10.0275
MA0084.10.0838
MA0087.10.231
MA0088.10.702
MA0090.17.04462e-5
MA0091.10.123
MA0092.10.0501
MA0093.10.0783
MA0099.20.361
MA0100.10.927
MA0101.19.17684e-4
MA0102.20.0039
MA0103.10.00242
MA0104.20.0415
MA0105.10.638
MA0106.10.163
MA0107.10.00149
MA0108.20.445
MA0111.10.086
MA0112.20.0714
MA0113.10.503
MA0114.10.0546
MA0115.10.0351
MA0116.10.219
MA0117.10.485
MA0119.10.0633
MA0122.10.72
MA0124.10.762
MA0125.10.869
MA0131.10.895
MA0135.10.167
MA0136.19.60864e-9
MA0137.20.777
MA0138.20.843
MA0139.10.494
MA0140.10.626
MA0141.10.357
MA0142.10.346
MA0143.10.699
MA0144.10.736
MA0145.10.544
MA0146.10.149
MA0147.10.284
MA0148.10.412
MA0149.10.89
MA0150.10.069
MA0152.10.0061
MA0153.10.224
MA0154.10.428
MA0155.10.397
MA0156.13.10264e-5
MA0157.10.641
MA0159.10.535
MA0160.10.0117
MA0162.10.0353
MA0163.10.0172
MA0164.10.937
MA0258.10.912
MA0259.10.356



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: CNhs10874

Novel motifP-value
10.9
100.538
1000.735
1010.508
1020.295
1030.277
1040.878
1050.156
1060.578
1070.0835
1080.813
1090.286
110.735
1100.729
1110.457
1120.949
1130.00468
1140.471
1150.0756
1160.104
1170.981
1180.322
1190.554
120.182
1200.184
1210.923
1220.101
1232.27635e-4
1240.0798
1250.948
1260.26
1270.0952
1280.809
1290.692
130.892
1300.622
1310.342
1320.764
1330.501
1340.647
1350.867
1360.221
1370.243
1380.0842
1390.801
140.14
1400.517
1410.903
1420.692
1430.754
1440.857
1450.267
1460.448
1470.128
1480.551
1490.0121
150.52
1500.0388
1510.456
1520.0828
1530.681
1540.935
1550.00345
1560.425
1570.096
1580.00212
1590.167
160.0363
1600.555
1610.834
1620.894
1630.9
1640.331
1650.612
1660.31
1670.757
1680.631
1690.254
170.628
180.199
190.0165
20.599
200.657
210.0673
220.608
230.675
240.677
250.359
260.79
270.894
280.248
290.309
30.729
300.458
310.66
326.11409e-11
330.866
340.694
350.687
360.0779
370.251
380.328
390.266
40.444
400.297
410.783
420.728
430.66
440.106
450.474
460.537
470.788
480.832
490.125
50.897
500.946
510.732
520.832
530.0691
540.905
550.243
560.653
570.955
580.238
590.268
60.284
600.645
610.591
620.743
630.547
640.592
650.657
660.703
670.721
680.876
690.606
70.47
700.797
710.301
720.957
730.0184
740.0721
750.394
760.313
770.0559
780.344
790.00357
80.217
800.497
810.793
820.984
830.75
840.418
850.965
860.607
870.017
880.608
890.0765
90.933
900.646
910.673
920.502
930.487
940.85
950.319
960.433
970.572
980.104
990.0075



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: CNhs10874


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)
0002547 (fibroblast of the aortic adventitia)
1000306 (fibroblast of tunica adventitia of artery)

UBERON: Anatomy
0000025 (tube)
0000055 (vessel)
0000060 (anatomical wall)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000415 (artery wall)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000947 (aorta)
0001009 (circulatory system)
0001062 (anatomical entity)
0001637 (artery)
0001981 (blood vessel)
0002049 (vasculature)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003509 (arterial blood vessel)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004571 (systemic arterial system)
0004572 (arterial system)
0004573 (systemic artery)
0004663 (aorta wall)
0004664 (aorta tunica adventitia)
0004872 (splanchnic layer of lateral plate mesoderm)
0004923 (organ component layer)
0005423 (developing anatomical structure)
0005734 (tunica adventitia of blood vessel)
0005742 (adventitia)
0006965 (vascular cord)
0007240 (tunica adventitia of artery)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)

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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