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FF:11283-116I5: 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 16:39, 29 March 2012


Name:Smooth Muscle Cells - Aortic, 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 stage39 years old adult
sexmale
age39
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 number1401(1)
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-0.0528
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-0.145
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
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: CNhs11085

Jaspar motifP-value
MA0002.20.929
MA0003.10.455
MA0004.10.721
MA0006.10.157
MA0007.10.475
MA0009.10.78
MA0014.10.182
MA0017.10.894
MA0018.20.00199
MA0019.10.338
MA0024.11.22947e-5
MA0025.10.196
MA0027.10.999
MA0028.10.00291
MA0029.10.434
MA0030.10.547
MA0031.10.315
MA0035.20.976
MA0038.10.764
MA0039.20.114
MA0040.10.956
MA0041.10.21
MA0042.10.384
MA0043.10.00335
MA0046.10.986
MA0047.20.74
MA0048.10.519
MA0050.15.41115e-21
MA0051.11.122e-15
MA0052.10.869
MA0055.10.965
MA0057.10.727
MA0058.10.606
MA0059.10.539
MA0060.10.073
MA0061.10.146
MA0062.29.46867e-6
MA0065.20.737
MA0066.10.753
MA0067.10.00469
MA0068.10.213
MA0069.10.645
MA0070.10.848
MA0071.10.4
MA0072.10.759
MA0073.10.778
MA0074.10.192
MA0076.10.00174
MA0077.10.273
MA0078.10.142
MA0079.20.879
MA0080.20.00563
MA0081.10.0502
MA0083.10.0242
MA0084.10.28
MA0087.10.365
MA0088.10.574
MA0090.10.00339
MA0091.10.328
MA0092.10.188
MA0093.10.751
MA0099.29.89241e-11
MA0100.10.0782
MA0101.10.124
MA0102.20.618
MA0103.10.0298
MA0104.20.366
MA0105.10.298
MA0106.10.205
MA0107.10.0147
MA0108.27.98466e-8
MA0111.10.0135
MA0112.20.0794
MA0113.10.384
MA0114.10.835
MA0115.10.97
MA0116.10.578
MA0117.10.307
MA0119.10.0391
MA0122.10.801
MA0124.10.319
MA0125.10.883
MA0131.10.325
MA0135.10.936
MA0136.10.0209
MA0137.20.955
MA0138.20.295
MA0139.10.507
MA0140.10.684
MA0141.10.726
MA0142.10.767
MA0143.10.452
MA0144.10.415
MA0145.10.146
MA0146.10.779
MA0147.10.611
MA0148.10.427
MA0149.10.332
MA0150.10.149
MA0152.10.229
MA0153.10.865
MA0154.10.21
MA0155.10.0284
MA0156.10.211
MA0157.10.877
MA0159.10.871
MA0160.10.712
MA0162.10.147
MA0163.10.284
MA0164.10.413
MA0258.10.177
MA0259.10.253



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: CNhs11085

Novel motifP-value
10.4
100.0997
1000.487
1010.594
1020.691
1030.673
1040.146
1050.929
1060.0343
1070.00597
1080.206
1090.605
110.533
1100.339
1110.223
1120.69
1130.166
1140.493
1150.602
1160.113
1170.873
1180.721
1190.754
120.81
1200.309
1210.245
1220.932
1230.00896
1240.669
1250.902
1260.421
1270.619
1280.175
1290.497
130.736
1300.191
1310.576
1320.483
1330.818
1340.967
1350.32
1360.135
1370.819
1380.908
1390.684
140.924
1400.764
1410.0422
1420.639
1430.198
1440.418
1450.507
1460.0673
1470.0182
1480.572
1490.256
150.878
1500.101
1510.362
1520.0378
1530.195
1540.702
1550.016
1560.592
1570.121
1580.0324
1590.407
160.141
1600.239
1610.786
1620.235
1630.762
1640.934
1650.331
1660.0363
1670.225
1680.963
1690.0951
170.295
180.0672
190.128
20.336
200.405
210.336
220.4
230.329
240.221
250.0539
260.364
270.824
280.136
290.989
30.614
300.415
310.526
328.92011e-6
330.972
340.271
350.649
360.327
370.39
380.961
390.14
40.667
400.145
410.86
420.961
430.243
440.686
450.169
460.456
470.831
480.808
490.919
50.942
500.51
510.671
520.692
530.268
540.565
550.24
560.434
570.858
580.334
590.194
60.25
600.568
610.424
620.536
630.401
640.855
650.252
660.849
670.857
680.24
690.405
70.263
700.463
710.885
720.229
730.0633
740.972
750.594
760.593
770.023
780.425
790.199
80.433
800.512
810.891
820.441
830.434
840.648
850.0748
860.655
870.0697
880.107
890.126
90.161
900.613
910.694
920.659
930.815
940.715
950.527
960.896
970.135
980.36
990.018



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: CNhs11085


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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