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FF:11290-117A3: 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 - Umbilical Artery, donor1
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 number1222
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-0.178
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-0.217
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: CNhs11091

Jaspar motifP-value
MA0002.20.212
MA0003.10.277
MA0004.10.484
MA0006.10.201
MA0007.10.14
MA0009.10.154
MA0014.10.915
MA0017.10.508
MA0018.20.00426
MA0019.10.303
MA0024.16.40844e-8
MA0025.10.336
MA0027.10.729
MA0028.10.915
MA0029.10.124
MA0030.10.709
MA0031.10.162
MA0035.20.2
MA0038.10.237
MA0039.20.927
MA0040.10.535
MA0041.10.343
MA0042.10.659
MA0043.10.057
MA0046.10.919
MA0047.20.681
MA0048.10.172
MA0050.11.31471e-9
MA0051.10.00519
MA0052.10.376
MA0055.10.36
MA0057.10.332
MA0058.10.241
MA0059.10.343
MA0060.10.00794
MA0061.10.395
MA0062.20.172
MA0065.20.301
MA0066.10.152
MA0067.10.0366
MA0068.10.99
MA0069.10.883
MA0070.10.72
MA0071.10.773
MA0072.10.229
MA0073.10.36
MA0074.10.236
MA0076.10.608
MA0077.10.0671
MA0078.10.142
MA0079.20.872
MA0080.20.00343
MA0081.10.182
MA0083.12.68064e-10
MA0084.10.68
MA0087.10.789
MA0088.10.424
MA0090.10.00124
MA0091.10.337
MA0092.10.0358
MA0093.10.449
MA0099.23.02487e-15
MA0100.10.161
MA0101.10.341
MA0102.20.0424
MA0103.10.278
MA0104.20.208
MA0105.10.352
MA0106.10.00805
MA0107.10.151
MA0108.25.51589e-5
MA0111.10.0595
MA0112.20.0126
MA0113.10.229
MA0114.10.646
MA0115.10.407
MA0116.10.586
MA0117.10.639
MA0119.10.115
MA0122.10.807
MA0124.10.343
MA0125.10.986
MA0131.10.416
MA0135.10.446
MA0136.10.189
MA0137.20.0596
MA0138.20.686
MA0139.10.65
MA0140.10.188
MA0141.10.771
MA0142.10.722
MA0143.10.93
MA0144.10.851
MA0145.10.113
MA0146.10.315
MA0147.10.527
MA0148.10.327
MA0149.10.479
MA0150.10.0339
MA0152.10.851
MA0153.10.973
MA0154.10.246
MA0155.10.0708
MA0156.10.776
MA0157.10.604
MA0159.10.544
MA0160.10.708
MA0162.10.0228
MA0163.10.0158
MA0164.10.756
MA0258.10.162
MA0259.10.904



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: CNhs11091

Novel motifP-value
10.602
100.449
1000.918
1010.392
1020.816
1030.266
1040.397
1050.64
1060.0158
1070.0302
1080.438
1090.102
110.12
1100.518
1110.744
1120.511
1130.109
1140.132
1150.903
1160.168
1170.728
1180.804
1190.0683
120.698
1200.11
1210.503
1220.469
1230.0103
1240.379
1250.829
1260.815
1270.561
1280.145
1290.989
130.991
1300.548
1310.0788
1320.906
1330.885
1340.177
1350.0216
1360.853
1370.631
1380.236
1390.0832
140.621
1400.483
1410.152
1420.869
1430.00956
1440.598
1450.189
1460.302
1470.206
1480.818
1490.121
150.421
1500.0797
1510.484
1520.0233
1530.605
1540.896
1550.0529
1560.789
1570.441
1580.0537
1590.362
160.205
1600.0915
1610.945
1620.435
1630.712
1640.472
1650.586
1660.915
1670.628
1680.48
1690.0701
170.0911
180.0983
190.129
20.34
200.534
210.797
220.203
230.0487
240.0927
250.496
260.676
270.724
280.416
290.308
30.439
300.594
310.372
322.73488e-4
330.487
340.482
350.493
360.477
370.054
380.914
390.42
40.333
400.185
410.302
420.587
430.31
440.713
450.342
460.218
470.335
480.224
490.498
50.487
500.479
510.889
520.416
530.48
540.777
550.569
560.385
570.276
580.589
590.116
60.981
600.375
610.906
620.83
630.14
640.52
650.353
660.687
670.342
680.205
690.624
70.994
700.0861
710.41
720.662
730.0109
740.954
750.357
760.458
770.0253
780.487
790.317
80.0853
800.376
810.652
820.274
830.979
840.786
850.0857
860.76
870.0187
880.0874
890.0661
90.268
900.993
910.743
920.338
930.291
940.74
950.295
960.908
970.402
980.457
990.00219



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: CNhs11091


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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