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FF:11212-116A6: 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 16:33, 29 March 2012


Name:Smooth Muscle Cells - Umbilical artery, donor0
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 stageNA
sexNA
ageNA
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 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-penis-0.166
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-0.213
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: CNhs10839

Jaspar motifP-value
MA0002.20.136
MA0003.10.301
MA0004.10.793
MA0006.10.178
MA0007.10.161
MA0009.10.497
MA0014.10.8
MA0017.10.362
MA0018.20.00665
MA0019.10.307
MA0024.14.3323e-7
MA0025.10.651
MA0027.10.689
MA0028.10.839
MA0029.10.0928
MA0030.10.744
MA0031.10.102
MA0035.20.182
MA0038.10.195
MA0039.20.563
MA0040.10.462
MA0041.10.327
MA0042.10.573
MA0043.10.0592
MA0046.10.725
MA0047.20.692
MA0048.10.187
MA0050.12.65088e-8
MA0051.10.00997
MA0052.10.437
MA0055.10.417
MA0057.10.334
MA0058.10.504
MA0059.10.196
MA0060.10.00814
MA0061.10.305
MA0062.20.0869
MA0065.20.166
MA0066.10.169
MA0067.10.0424
MA0068.10.293
MA0069.10.64
MA0070.10.647
MA0071.10.7
MA0072.10.251
MA0073.10.507
MA0074.10.11
MA0076.10.364
MA0077.10.122
MA0078.10.175
MA0079.20.809
MA0080.20.00233
MA0081.10.192
MA0083.16.0777e-9
MA0084.10.593
MA0087.10.715
MA0088.10.537
MA0090.10.00109
MA0091.10.27
MA0092.10.0862
MA0093.10.727
MA0099.25.26292e-13
MA0100.10.218
MA0101.10.467
MA0102.20.0423
MA0103.10.665
MA0104.20.431
MA0105.10.23
MA0106.10.00697
MA0107.10.283
MA0108.28.27421e-4
MA0111.10.105
MA0112.20.00141
MA0113.10.283
MA0114.10.404
MA0115.10.635
MA0116.10.242
MA0117.10.959
MA0119.10.0653
MA0122.10.978
MA0124.10.602
MA0125.10.465
MA0131.10.474
MA0135.10.552
MA0136.10.0923
MA0137.20.06
MA0138.20.8
MA0139.10.514
MA0140.10.228
MA0141.10.406
MA0142.10.989
MA0143.10.633
MA0144.10.643
MA0145.10.0934
MA0146.10.361
MA0147.10.767
MA0148.10.267
MA0149.10.417
MA0150.10.0481
MA0152.10.896
MA0153.10.947
MA0154.10.0887
MA0155.10.0982
MA0156.10.761
MA0157.10.505
MA0159.10.289
MA0160.10.562
MA0162.10.0316
MA0163.10.0024
MA0164.10.593
MA0258.10.0597
MA0259.10.794



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: CNhs10839

Novel motifP-value
10.435
100.542
1000.961
1010.573
1020.995
1030.215
1040.423
1050.865
1060.0175
1070.0334
1080.497
1090.0713
110.0677
1100.366
1110.518
1120.575
1130.178
1140.0765
1150.824
1160.207
1170.413
1180.818
1190.16
120.886
1200.07
1210.558
1220.392
1230.0972
1240.688
1250.745
1260.915
1270.885
1280.146
1290.706
130.837
1300.89
1310.134
1320.788
1330.715
1340.0998
1350.0615
1360.892
1370.705
1380.449
1390.194
140.673
1400.618
1410.175
1421
1430.00109
1440.863
1450.362
1460.217
1470.345
1480.571
1490.215
150.324
1500.11
1510.689
1520.0154
1530.473
1540.716
1550.0953
1560.852
1570.403
1580.124
1590.457
160.119
1600.1
1610.742
1620.323
1630.564
1640.231
1650.425
1660.822
1670.704
1680.327
1690.0489
170.103
180.0713
190.0737
20.266
200.728
210.693
220.197
230.147
240.155
250.618
260.521
270.579
280.445
290.38
30.321
300.776
310.301
322.28569e-4
330.602
340.496
350.337
360.53
370.0308
380.796
390.376
40.389
400.134
410.3
420.616
430.324
440.539
450.332
460.148
470.241
480.308
490.413
50.482
500.473
510.937
520.51
530.354
540.612
550.531
560.333
570.416
580.816
590.0268
60.988
600.44
610.879
620.606
630.12
640.414
650.209
660.498
670.557
680.299
690.896
70.922
700.235
710.412
720.92
730.00746
740.929
750.328
760.986
770.0289
780.771
790.166
80.0458
800.357
810.443
820.265
830.581
840.648
850.157
860.454
870.0228
880.0794
890.0684
90.415
900.671
910.298
920.35
930.638
940.627
950.131
960.695
970.211
980.464
990.00826



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: CNhs10839


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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