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FF:11401-118D6: 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 17:06, 29 March 2012


Name:Fibroblast - Aortic Adventitial, donor3
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 stage19 years old adult
sexfemale
age19
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-penis0.163
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-lymphoma0.323
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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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: CNhs12011

Jaspar motifP-value
MA0002.20.469
MA0003.10.649
MA0004.10.0777
MA0006.10.0878
MA0007.10.811
MA0009.10.968
MA0014.10.487
MA0017.10.424
MA0018.22.63157e-6
MA0019.10.618
MA0024.10.129
MA0025.10.0126
MA0027.10.857
MA0028.16.4828e-4
MA0029.10.804
MA0030.10.296
MA0031.10.0851
MA0035.20.437
MA0038.10.253
MA0039.20.13
MA0040.10.818
MA0041.10.442
MA0042.10.771
MA0043.13.84034e-6
MA0046.10.0843
MA0047.20.198
MA0048.10.105
MA0050.10.213
MA0051.10.46
MA0052.10.205
MA0055.10.936
MA0057.10.157
MA0058.10.0107
MA0059.10.264
MA0060.10.0935
MA0061.10.0938
MA0062.26.13077e-8
MA0065.20.11
MA0066.10.305
MA0067.10.00633
MA0068.10.492
MA0069.10.36
MA0070.10.637
MA0071.10.463
MA0072.10.23
MA0073.10.694
MA0074.10.183
MA0076.15.62862e-4
MA0077.10.642
MA0078.10.8
MA0079.20.879
MA0080.24.75607e-4
MA0081.10.0348
MA0083.10.0562
MA0084.10.268
MA0087.10.711
MA0088.10.256
MA0090.10.00658
MA0091.10.41
MA0092.10.389
MA0093.10.0724
MA0099.20.562
MA0100.10.706
MA0101.10.00803
MA0102.20.0601
MA0103.10.00248
MA0104.20.00268
MA0105.10.141
MA0106.10.963
MA0107.10.0329
MA0108.23.02298e-5
MA0111.10.322
MA0112.20.403
MA0113.10.603
MA0114.10.0538
MA0115.10.216
MA0116.10.718
MA0117.10.389
MA0119.10.585
MA0122.10.443
MA0124.10.0648
MA0125.10.546
MA0131.10.277
MA0135.10.927
MA0136.11.37725e-6
MA0137.20.994
MA0138.20.994
MA0139.10.634
MA0140.10.548
MA0141.10.35
MA0142.10.507
MA0143.10.79
MA0144.10.606
MA0145.10.783
MA0146.10.632
MA0147.10.0195
MA0148.10.473
MA0149.10.458
MA0150.10.201
MA0152.14.6135e-4
MA0153.10.938
MA0154.10.988
MA0155.10.123
MA0156.11.55046e-4
MA0157.10.209
MA0159.10.453
MA0160.10.0499
MA0162.10.326
MA0163.10.409
MA0164.10.853
MA0258.10.772
MA0259.10.0374



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: CNhs12011

Novel motifP-value
10.342
100.508
1000.356
1010.235
1020.382
1030.955
1040.906
1050.0838
1060.22
1070.0458
1080.759
1090.912
110.991
1100.449
1110.508
1120.774
1130.011
1140.946
1150.0184
1160.0283
1170.136
1180.239
1190.145
120.302
1200.185
1210.998
1220.103
1236.68814e-6
1240.105
1250.725
1260.289
1270.395
1280.441
1290.623
130.488
1300.24
1310.739
1320.514
1330.89
1340.501
1350.334
1360.33
1370.479
1380.523
1390.135
140.181
1400.499
1410.491
1420.826
1430.953
1440.618
1450.39
1460.965
1470.132
1480.608
1490.107
150.249
1500.0563
1510.561
1520.0259
1530.644
1540.733
1550.0319
1560.189
1570.278
1580.00176
1590.199
160.0362
1600.738
1610.991
1620.615
1630.702
1640.746
1650.771
1660.0572
1670.195
1680.842
1690.133
170.942
180.277
190.0345
20.207
200.239
210.051
220.315
230.38
240.519
250.236
260.375
270.532
280.264
290.812
30.907
300.249
310.691
321.74586e-13
330.886
340.633
350.196
360.025
370.746
380.477
390.223
40.564
400.18
410.111
420.338
430.66
440.0187
450.949
460.615
470.528
480.983
490.111
50.899
500.864
510.938
520.953
530.0465
540.737
550.79
560.513
570.158
580.219
590.205
60.662
600.684
610.375
620.69
630.691
640.575
650.532
660.888
670.924
680.9
690.485
70.0867
700.658
710.998
720.827
730.0557
740.0247
750.33
760.173
770.137
780.0194
790.0025
80.286
800.376
810.928
820.217
830.743
840.885
850.67
860.872
870.115
880.44
890.255
90.279
900.0805
910.784
920.31
930.483
940.555
950.394
960.677
970.624
980.0553
990.014



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: CNhs12011


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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