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FF:11360-117I1: 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, donor2
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 stage40 years old adult
sexmale
age40
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 number1347
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-0.207
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-0.221
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11305

Jaspar motifP-value
MA0002.20.14
MA0003.10.195
MA0004.10.85
MA0006.10.266
MA0007.10.368
MA0009.10.695
MA0014.10.872
MA0017.10.329
MA0018.20.00104
MA0019.10.453
MA0024.13.14441e-5
MA0025.10.376
MA0027.10.751
MA0028.10.685
MA0029.10.265
MA0030.10.208
MA0031.10.0343
MA0035.20.227
MA0038.10.225
MA0039.20.385
MA0040.10.507
MA0041.10.442
MA0042.10.915
MA0043.10.0016
MA0046.10.353
MA0047.20.978
MA0048.10.913
MA0050.16.66787e-5
MA0051.10.172
MA0052.10.931
MA0055.10.417
MA0057.10.11
MA0058.10.95
MA0059.10.0817
MA0060.10.0516
MA0061.10.376
MA0062.20.402
MA0065.20.232
MA0066.10.307
MA0067.10.0161
MA0068.10.159
MA0069.10.586
MA0070.10.721
MA0071.10.722
MA0072.10.495
MA0073.10.472
MA0074.10.507
MA0076.10.466
MA0077.10.145
MA0078.10.194
MA0079.20.764
MA0080.20.154
MA0081.10.725
MA0083.11.00625e-4
MA0084.10.577
MA0087.10.571
MA0088.10.466
MA0090.10.0102
MA0091.10.0446
MA0092.10.0584
MA0093.10.822
MA0099.21.56659e-17
MA0100.10.155
MA0101.10.755
MA0102.20.00615
MA0103.10.422
MA0104.20.722
MA0105.10.282
MA0106.10.126
MA0107.10.456
MA0108.27.41789e-7
MA0111.10.0521
MA0112.20.00455
MA0113.10.195
MA0114.10.383
MA0115.10.943
MA0116.10.13
MA0117.10.402
MA0119.10.055
MA0122.10.63
MA0124.10.502
MA0125.10.704
MA0131.10.311
MA0135.10.954
MA0136.10.465
MA0137.20.353
MA0138.20.872
MA0139.10.751
MA0140.10.111
MA0141.10.538
MA0142.10.55
MA0143.10.777
MA0144.10.577
MA0145.10.0803
MA0146.10.158
MA0147.10.751
MA0148.10.62
MA0149.10.404
MA0150.10.0204
MA0152.10.474
MA0153.10.595
MA0154.10.125
MA0155.10.0975
MA0156.10.731
MA0157.10.391
MA0159.10.0771
MA0160.10.562
MA0162.10.069
MA0163.10.036
MA0164.10.565
MA0258.10.122
MA0259.10.989



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: CNhs11305

Novel motifP-value
10.426
100.4
1000.938
1010.993
1020.983
1030.517
1040.256
1050.193
1060.025
1070.0319
1080.477
1090.0612
110.0939
1100.333
1110.502
1120.38
1130.302
1140.141
1150.97
1160.148
1170.963
1180.931
1190.175
120.627
1200.202
1210.685
1220.531
1230.0776
1240.71
1250.928
1260.7
1270.184
1280.146
1290.815
130.612
1300.164
1310.257
1320.935
1330.568
1340.151
1350.152
1360.585
1370.774
1380.826
1390.519
140.999
1400.599
1410.387
1420.96
1430.0082
1440.79
1450.117
1460.433
1470.0977
1480.44
1490.1
150.376
1500.204
1510.291
1520.0253
1530.883
1540.489
1550.0406
1560.929
1570.795
1580.169
1590.527
160.268
1600.0705
1610.444
1620.923
1631
1640.692
1650.64
1660.441
1670.821
1680.297
1690.0452
170.0517
180.0472
190.0911
20.406
200.315
210.575
220.137
230.136
240.157
250.498
260.193
270.452
280.293
290.519
30.459
300.164
310.547
320.0344
330.938
340.347
350.694
360.799
370.131
380.37
390.312
40.458
400.145
410.319
420.519
430.257
440.937
450.191
460.138
470.454
480.166
490.396
50.663
500.411
510.865
520.312
530.833
540.531
550.134
560.423
570.376
580.893
590.103
60.756
600.351
610.846
620.951
630.158
640.287
650.117
660.365
670.695
680.163
690.376
70.808
700.0436
710.177
720.667
730.00854
740.905
750.538
760.82
770.0164
780.722
790.3
80.0358
800.221
810.354
820.385
830.524
840.885
850.146
860.836
870.08
880.0903
890.0262
90.256
900.878
910.189
920.535
930.685
940.438
950.299
960.797
970.16
980.729
990.0167



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: CNhs11305


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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