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FF:11367-117I8: 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 17:05, 29 March 2012


Name:Smooth Muscle Cells - Umbilical Artery, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueumbilical artery
dev stageinfant
sexfemale
ageneonatal
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 number1438
catalog numberCA252-R10n
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-penis0
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-lymphoma0.0443
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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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: CNhs11991

Jaspar motifP-value
MA0002.20.152
MA0003.10.291
MA0004.10.265
MA0006.10.0864
MA0007.10.218
MA0009.10.505
MA0014.10.896
MA0017.10.397
MA0018.20.00885
MA0019.10.171
MA0024.10.209
MA0025.10.381
MA0027.10.864
MA0028.10.498
MA0029.10.33
MA0030.10.175
MA0031.10.00457
MA0035.20.712
MA0038.10.459
MA0039.20.742
MA0040.10.756
MA0041.10.562
MA0042.10.869
MA0043.10.0218
MA0046.10.92
MA0047.20.304
MA0048.10.0721
MA0050.10.00168
MA0051.10.0528
MA0052.10.786
MA0055.10.232
MA0057.10.122
MA0058.10.0561
MA0059.10.775
MA0060.10.53
MA0061.10.109
MA0062.20.366
MA0065.20.168
MA0066.10.313
MA0067.10.0039
MA0068.10.802
MA0069.10.914
MA0070.10.925
MA0071.10.495
MA0072.10.662
MA0073.10.552
MA0074.10.133
MA0076.10.141
MA0077.10.159
MA0078.10.445
MA0079.20.92
MA0080.20.361
MA0081.10.208
MA0083.15.54877e-12
MA0084.10.797
MA0087.10.72
MA0088.10.482
MA0090.10.0237
MA0091.10.452
MA0092.10.0975
MA0093.10.202
MA0099.27.45947e-9
MA0100.10.144
MA0101.10.0932
MA0102.20.0961
MA0103.10.12
MA0104.20.165
MA0105.10.18
MA0106.10.285
MA0107.10.0538
MA0108.23.47534e-17
MA0111.10.224
MA0112.20.0426
MA0113.10.649
MA0114.10.706
MA0115.10.225
MA0116.10.189
MA0117.10.835
MA0119.10.17
MA0122.10.618
MA0124.10.795
MA0125.10.356
MA0131.10.925
MA0135.10.269
MA0136.10.497
MA0137.20.327
MA0138.20.291
MA0139.10.853
MA0140.10.426
MA0141.10.601
MA0142.10.717
MA0143.10.185
MA0144.10.266
MA0145.10.116
MA0146.10.305
MA0147.10.36
MA0148.10.44
MA0149.10.885
MA0150.10.323
MA0152.10.989
MA0153.10.987
MA0154.10.21
MA0155.10.0607
MA0156.10.147
MA0157.10.068
MA0159.10.886
MA0160.10.741
MA0162.10.0211
MA0163.10.0545
MA0164.10.85
MA0258.10.318
MA0259.10.471



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: CNhs11991

Novel motifP-value
10.96
100.738
1000.947
1010.222
1020.954
1030.539
1040.591
1050.438
1060.0532
1070.0199
1080.33
1090.0568
110.112
1100.172
1110.85
1120.343
1130.171
1140.681
1150.164
1160.00392
1170.679
1180.92
1190.18
120.238
1200.242
1210.62
1220.912
1230.0189
1240.247
1250.413
1260.721
1270.191
1280.124
1290.676
130.508
1300.643
1310.278
1320.981
1330.71
1340.272
1350.0248
1360.192
1370.612
1380.408
1390.564
140.377
1400.939
1410.46
1420.082
1430.00123
1440.592
1450.276
1460.249
1470.52
1480.613
1490.0993
150.714
1500.162
1510.776
1520.0316
1530.517
1540.533
1550.219
1560.668
1570.119
1580.0137
1590.247
160.0865
1600.122
1610.177
1620.674
1630.74
1640.304
1650.966
1660.521
1670.199
1680.716
1690.0774
170.173
180.225
190.0383
20.184
200.328
210.65
220.345
230.258
240.704
250.647
260.294
270.533
280.29
290.403
30.475
300.429
310.466
324.96496e-6
330.454
340.151
350.941
360.663
370.0852
380.999
390.365
40.577
400.0658
410.793
420.76
430.343
440.0839
450.476
460.393
470.646
480.335
490.794
50.576
500.68
510.773
520.414
530.242
540.52
550.759
560.572
570.705
580.658
590.0439
60.677
600.477
610.882
620.73
630.301
640.306
650.233
660.847
670.867
680.329
690.69
70.819
700.787
710.422
720.69
730.00617
740.597
750.374
760.154
770.00132
780.689
790.00129
80.0392
800.337
810.565
820.698
830.621
840.717
850.215
860.753
870.00795
880.122
890.207
90.0881
900.101
910.224
920.957
930.696
940.862
950.147
960.863
970.87
980.789
990.00136



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: CNhs11991


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)
0002594 (smooth muscle cell of the umbilical artery)

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)
0001009 (circulatory system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001310 (umbilical artery)
0001637 (artery)
0001981 (blood vessel)
0002036 (striated muscle tissue)
0002049 (vasculature)
0002050 (embryonic structure)
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)
0004290 (dermomyotome)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004572 (arterial system)
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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