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FF:14313-155D2: 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 17:19, 29 March 2012


Name:Smooth Muscle Cells - Aortic, donor0 (cytoplasmic fraction)
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 numberNA
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-0.205
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-0.31
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: CNhs12401

Jaspar motifP-value
MA0002.20.635
MA0003.10.201
MA0004.10.402
MA0006.10.605
MA0007.10.281
MA0009.10.414
MA0014.10.667
MA0017.10.364
MA0018.23.59426e-5
MA0019.10.4
MA0024.16.22495e-6
MA0025.10.0311
MA0027.10.365
MA0028.10.595
MA0029.10.827
MA0030.10.0625
MA0031.10.164
MA0035.20.734
MA0038.12.95893e-4
MA0039.20.161
MA0040.10.721
MA0041.10.456
MA0042.10.69
MA0043.10.0017
MA0046.10.289
MA0047.20.443
MA0048.10.372
MA0050.11.3873e-7
MA0051.10.00198
MA0052.10.0426
MA0055.10.886
MA0057.10.0639
MA0058.10.227
MA0059.10.232
MA0060.13.84945e-11
MA0061.10.431
MA0062.20.0235
MA0065.20.0454
MA0066.10.0697
MA0067.10.0376
MA0068.10.112
MA0069.10.103
MA0070.10.919
MA0071.10.156
MA0072.10.835
MA0073.10.851
MA0074.10.265
MA0076.10.224
MA0077.10.847
MA0078.10.937
MA0079.20.938
MA0080.21.33627e-4
MA0081.10.118
MA0083.10.056
MA0084.10.67
MA0087.10.434
MA0088.10.208
MA0090.10.0943
MA0091.10.0322
MA0092.10.0751
MA0093.10.385
MA0099.20.218
MA0100.10.291
MA0101.10.215
MA0102.20.0126
MA0103.10.824
MA0104.20.767
MA0105.10.0114
MA0106.10.0247
MA0107.10.283
MA0108.20.401
MA0111.10.786
MA0112.29.90285e-4
MA0113.10.174
MA0114.10.546
MA0115.10.511
MA0116.10.0091
MA0117.10.765
MA0119.10.0489
MA0122.10.956
MA0124.10.252
MA0125.10.0978
MA0131.10.465
MA0135.10.673
MA0136.14.29121e-5
MA0137.20.781
MA0138.20.552
MA0139.10.32
MA0140.10.653
MA0141.10.0262
MA0142.10.341
MA0143.10.802
MA0144.10.609
MA0145.10.169
MA0146.10.114
MA0147.10.754
MA0148.10.788
MA0149.10.305
MA0150.10.664
MA0152.10.383
MA0153.10.799
MA0154.10.0443
MA0155.10.212
MA0156.10.00415
MA0157.10.56
MA0159.10.0495
MA0160.10.534
MA0162.10.0858
MA0163.15.34134e-5
MA0164.10.414
MA0258.10.0263
MA0259.10.301



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: CNhs12401

Novel motifP-value
10.0749
100.37
1000.901
1010.981
1020.826
1030.0367
1040.539
1050.669
1060.0366
1070.784
1080.223
1090.0359
110.0535
1100.144
1110.295
1120.107
1130.101
1140.00252
1152.7549e-4
1160.12
1170.244
1180.292
1190.251
120.701
1200.0378
1210.716
1220.46
1230.0882
1240.464
1250.951
1260.797
1270.15
1280.0918
1290.364
130.821
1300.631
1310.418
1320.994
1330.564
1340.473
1350.411
1360.982
1370.233
1380.505
1390.0451
140.58
1400.727
1410.825
1420.491
1430.0513
1440.735
1450.733
1460.929
1470.169
1480.375
1490.0504
150.352
1500.514
1510.572
1520.0827
1530.184
1540.582
1550.235
1560.878
1570.834
1580.0964
1590.19
160.037
1600.128
1610.519
1620.913
1630.693
1640.106
1650.5
1660.875
1670.856
1680.217
1690.0211
170.304
180.031
190.0894
20.269
200.567
210.135
220.146
230.0401
240.763
250.841
260.198
270.189
280.4
290.187
30.15
300.69
310.317
321.14807e-4
330.496
340.561
350.344
360.551
370.0584
380.607
390.229
40.615
400.66
410.923
420.287
430.305
440.0249
450.644
460.0277
470.192
480.415
490.345
50.571
500.752
510.497
520.681
530.51
540.538
550.193
560.406
570.55
580.4
590.00844
60.668
600.363
610.539
620.106
630.158
640.321
650.134
660.406
670.396
680.121
690.254
70.774
700.0131
710.0571
720.997
730.0796
740.135
750.197
760.705
770.00441
780.428
793.81072e-5
80.0387
800.798
810.389
820.0294
830.343
840.13
850.0225
860.433
870.164
880.685
890.00352
90.488
900.32
910.222
920.103
930.602
940.0427
950.135
960.768
970.738
980.836
990.0247



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: CNhs12401


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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