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FF:11439-118H8: 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 17:08, 29 March 2012


Name:Smooth Muscle Cells - Umbilical Artery, donor3
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 number1447
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-0.0997
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-lymphoma0.0365
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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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: CNhs12049

Jaspar motifP-value
MA0002.20.955
MA0003.10.288
MA0004.10.493
MA0006.10.191
MA0007.10.108
MA0009.10.286
MA0014.10.704
MA0017.10.735
MA0018.20.00188
MA0019.10.397
MA0024.10.422
MA0025.10.102
MA0027.10.949
MA0028.10.368
MA0029.10.286
MA0030.10.00283
MA0031.11.4406e-4
MA0035.20.678
MA0038.10.756
MA0039.20.972
MA0040.10.395
MA0041.10.629
MA0042.10.758
MA0043.11.24394e-4
MA0046.10.33
MA0047.20.21
MA0048.10.0738
MA0050.14.57502e-8
MA0051.18.62044e-4
MA0052.10.953
MA0055.10.0235
MA0057.10.116
MA0058.10.166
MA0059.10.349
MA0060.10.406
MA0061.10.973
MA0062.20.598
MA0065.20.243
MA0066.10.238
MA0067.10.0067
MA0068.10.649
MA0069.10.786
MA0070.10.405
MA0071.10.404
MA0072.10.828
MA0073.10.706
MA0074.10.288
MA0076.10.819
MA0077.10.0893
MA0078.10.733
MA0079.20.753
MA0080.25.36038e-6
MA0081.10.0663
MA0083.14.4469e-5
MA0084.10.997
MA0087.10.773
MA0088.10.337
MA0090.10.0409
MA0091.10.231
MA0092.10.341
MA0093.10.428
MA0099.24.32103e-6
MA0100.10.237
MA0101.10.449
MA0102.20.00307
MA0103.10.313
MA0104.20.407
MA0105.10.655
MA0106.10.205
MA0107.10.673
MA0108.24.14041e-4
MA0111.10.0419
MA0112.20.0479
MA0113.10.334
MA0114.10.905
MA0115.10.685
MA0116.10.596
MA0117.10.432
MA0119.10.352
MA0122.10.589
MA0124.10.486
MA0125.10.41
MA0131.10.729
MA0135.10.187
MA0136.13.19738e-5
MA0137.20.0229
MA0138.20.397
MA0139.10.433
MA0140.10.921
MA0141.10.2
MA0142.10.747
MA0143.10.305
MA0144.10.517
MA0145.10.272
MA0146.10.218
MA0147.10.897
MA0148.10.343
MA0149.10.597
MA0150.10.95
MA0152.10.731
MA0153.10.856
MA0154.10.388
MA0155.10.0555
MA0156.10.135
MA0157.10.0062
MA0159.10.848
MA0160.10.977
MA0162.10.0465
MA0163.10.0532
MA0164.10.519
MA0258.10.108
MA0259.10.699



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: CNhs12049

Novel motifP-value
10.744
100.476
1000.415
1010.0651
1020.798
1030.412
1040.294
1050.801
1060.13
1070.0217
1080.973
1090.0232
110.0633
1100.0879
1110.639
1120.432
1130.0311
1140.868
1150.02
1160.0169
1170.42
1180.943
1190.499
120.683
1200.0492
1210.436
1220.731
1230.0202
1240.465
1250.84
1260.959
1270.796
1280.352
1290.589
130.674
1300.478
1310.441
1320.348
1330.713
1340.284
1350.509
1360.447
1370.0723
1380.382
1390.878
140.354
1400.712
1410.57
1420.567
1430.00845
1440.729
1450.45
1460.672
1470.0611
1480.362
1490.0383
150.662
1500.0753
1510.919
1520.0427
1530.399
1540.26
1550.1
1560.934
1570.143
1580.0157
1590.415
160.163
1600.017
1610.371
1620.169
1630.928
1640.711
1650.321
1660.37
1670.328
1680.963
1690.0848
170.16
180.368
190.0808
20.236
200.464
210.648
220.186
230.476
240.318
250.513
260.225
270.345
280.166
290.473
30.635
300.233
310.577
322.88729e-7
330.753
340.236
350.79
360.735
370.0795
380.96
390.257
40.524
400.0766
410.776
420.86
430.669
440.1
450.487
460.169
470.475
480.136
490.725
50.556
500.386
510.986
520.867
530.268
540.992
550.702
560.497
570.878
580.327
590.0223
60.996
600.806
610.599
620.707
630.333
640.167
650.167
660.445
670.905
680.00584
690.377
70.744
700.973
710.546
720.317
730.00859
740.224
750.394
760.207
770.0108
780.746
790.0061
80.0479
800.933
810.934
820.694
830.749
840.742
850.845
860.872
870.0129
880.159
890.367
90.291
900.0759
910.827
920.777
930.595
940.851
950.0611
960.594
970.928
980.987
993.31206e-4



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: CNhs12049


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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