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FF:11432-118H1: 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 16:44, 29 March 2012


Name:Smooth Muscle Cells - Aortic, 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 stage54 years old adult
sexmale
age54
cell typesmooth muscle cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1441
catalog numberCA354-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-penis-0.15
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-0.0394
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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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: CNhs11309

Jaspar motifP-value
MA0002.20.435
MA0003.10.343
MA0004.10.469
MA0006.10.251
MA0007.10.0643
MA0009.10.324
MA0014.10.934
MA0017.10.827
MA0018.20.0155
MA0019.10.278
MA0024.10.00895
MA0025.10.928
MA0027.10.316
MA0028.10.986
MA0029.10.308
MA0030.10.936
MA0031.10.22
MA0035.20.981
MA0038.10.759
MA0039.20.758
MA0040.10.47
MA0041.10.332
MA0042.10.694
MA0043.10.0361
MA0046.10.233
MA0047.20.137
MA0048.10.406
MA0050.11.17949e-6
MA0051.10.0199
MA0052.10.547
MA0055.10.22
MA0057.10.647
MA0058.10.222
MA0059.10.862
MA0060.10.413
MA0061.10.548
MA0062.20.161
MA0065.20.242
MA0066.10.867
MA0067.10.0447
MA0068.10.754
MA0069.10.474
MA0070.10.401
MA0071.10.891
MA0072.10.56
MA0073.10.94
MA0074.10.62
MA0076.10.845
MA0077.10.524
MA0078.10.472
MA0079.20.236
MA0080.20.00256
MA0081.10.357
MA0083.12.53219e-4
MA0084.10.514
MA0087.10.639
MA0088.10.372
MA0090.10.00867
MA0091.10.0468
MA0092.10.139
MA0093.10.523
MA0099.24.50476e-17
MA0100.10.199
MA0101.10.732
MA0102.20.845
MA0103.10.0123
MA0104.20.0887
MA0105.10.956
MA0106.10.102
MA0107.10.63
MA0108.27.79023e-8
MA0111.10.0128
MA0112.20.506
MA0113.10.635
MA0114.10.721
MA0115.10.596
MA0116.10.402
MA0117.10.597
MA0119.10.206
MA0122.10.299
MA0124.10.656
MA0125.10.522
MA0131.10.823
MA0135.10.38
MA0136.10.117
MA0137.20.634
MA0138.20.217
MA0139.10.822
MA0140.10.736
MA0141.10.918
MA0142.10.335
MA0143.10.922
MA0144.10.661
MA0145.10.107
MA0146.10.382
MA0147.10.35
MA0148.10.118
MA0149.10.583
MA0150.10.0316
MA0152.10.558
MA0153.10.711
MA0154.10.968
MA0155.10.198
MA0156.10.818
MA0157.10.657
MA0159.10.998
MA0160.10.584
MA0162.10.168
MA0163.10.25
MA0164.10.991
MA0258.10.731
MA0259.10.743



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: CNhs11309

Novel motifP-value
10.489
100.0584
1000.241
1010.111
1020.955
1030.914
1040.488
1050.316
1060.212
1070.265
1080.845
1090.295
110.141
1100.646
1110.119
1120.685
1130.0502
1140.994
1150.664
1160.0305
1170.575
1180.188
1190.832
120.813
1200.511
1210.581
1220.6
1230.0225
1240.741
1250.702
1260.808
1270.57
1280.658
1290.815
130.109
1300.0191
1310.0544
1320.777
1330.609
1340.185
1350.416
1360.66
1370.809
1380.355
1390.353
140.374
1400.201
1410.0133
1420.76
1430.0203
1440.853
1450.121
1460.0722
1470.665
1480.532
1490.55
150.742
1500.515
1510.799
1520.0174
1530.942
1540.85
1550.0739
1560.591
1570.748
1580.0398
1590.553
160.438
1600.591
1610.415
1620.88
1630.721
1640.911
1650.396
1660.709
1670.429
1680.631
1690.278
170.239
180.152
190.442
20.775
200.157
210.776
220.178
230.0267
240.174
250.409
260.279
270.978
280.147
290.993
30.758
300.0509
310.991
320.31
330.975
340.52
350.456
360.316
370.732
380.65
390.44
40.934
400.908
410.664
420.821
430.392
440.432
450.239
460.394
470.94
480.547
490.841
50.888
500.263
510.776
520.325
530.232
540.959
550.513
560.886
570.844
580.46
590.36
60.655
600.889
610.659
620.66
630.434
640.498
650.215
660.109
670.444
680.683
690.228
70.509
700.811
710.646
720.441
730.00273
740.468
750.985
760.943
770.188
780.256
790.862
80.632
800.794
810.486
820.959
830.893
840.581
850.586
860.651
870.0951
880.378
890.501
90.13
900.608
910.462
920.89
930.981
940.416
950.873
960.987
970.309
980.272
990.0267



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: CNhs11309


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)
0000056 (myoblast)
0000183 (contractile cell)
0000187 (muscle cell)
0000192 (smooth muscle cell)
0000211 (electrically active cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000355 (multi-potent skeletal muscle stem cell)
0000359 (vascular associated smooth muscle cell)
0000393 (electrically responsive cell)
0000514 (smooth muscle myoblast)
0000548 (animal cell)
0000680 (muscle precursor cell)
0000723 (somatic stem cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002539 (aortic smooth muscle cell)

UBERON: Anatomy
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000119 (cell layer)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000947 (aorta)
0001009 (circulatory system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001135 (smooth muscle tissue)
0001637 (artery)
0001981 (blood vessel)
0002036 (striated muscle tissue)
0002049 (vasculature)
0002050 (embryonic structure)
0002111 (artery smooth muscle tissue)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003081 (lateral plate mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0003509 (arterial blood vessel)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004178 (aorta smooth muscle tissue)
0004237 (blood vessel smooth muscle)
0004290 (dermomyotome)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004571 (systemic arterial system)
0004572 (arterial system)
0004573 (systemic artery)
0004695 (arterial system smooth muscle)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006965 (vascular cord)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)
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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