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FF:11621-122B1: 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 17:22, 29 March 2012


Name:Smooth Muscle Cells - Umbilical Vein, 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 vein
dev stageNA
sexNA
ageNA
cell typesmooth muscle cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number6757
catalog numberSC8025
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-0.199
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-0.153
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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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: CNhs12569

Jaspar motifP-value
MA0002.20.846
MA0003.10.227
MA0004.10.149
MA0006.10.068
MA0007.10.227
MA0009.10.359
MA0014.10.74
MA0017.10.414
MA0018.26.37147e-5
MA0019.10.265
MA0024.15.57411e-6
MA0025.10.0247
MA0027.10.919
MA0028.10.798
MA0029.10.434
MA0030.10.0135
MA0031.10.0502
MA0035.20.192
MA0038.10.235
MA0039.20.993
MA0040.10.593
MA0041.10.65
MA0042.10.621
MA0043.10.0573
MA0046.10.594
MA0047.20.24
MA0048.10.0946
MA0050.11.62217e-7
MA0051.10.00816
MA0052.10.0581
MA0055.10.112
MA0057.10.851
MA0058.10.065
MA0059.10.56
MA0060.10.615
MA0061.10.831
MA0062.22.3094e-4
MA0065.20.3
MA0066.10.317
MA0067.11.65124e-4
MA0068.10.894
MA0069.10.63
MA0070.10.344
MA0071.10.167
MA0072.10.875
MA0073.10.412
MA0074.10.839
MA0076.10.0606
MA0077.10.79
MA0078.10.588
MA0079.20.686
MA0080.27.0633e-9
MA0081.10.00972
MA0083.10.00325
MA0084.10.18
MA0087.10.546
MA0088.10.251
MA0090.14.26545e-5
MA0091.10.0435
MA0092.10.0668
MA0093.10.146
MA0099.20.794
MA0100.10.855
MA0101.10.654
MA0102.20.407
MA0103.10.0699
MA0104.20.39
MA0105.10.257
MA0106.10.0186
MA0107.10.735
MA0108.20.0208
MA0111.10.732
MA0112.20.0168
MA0113.10.0362
MA0114.10.215
MA0115.10.152
MA0116.10.484
MA0117.10.853
MA0119.10.117
MA0122.10.658
MA0124.10.372
MA0125.10.984
MA0131.10.342
MA0135.10.193
MA0136.14.72439e-8
MA0137.20.266
MA0138.20.744
MA0139.10.946
MA0140.10.134
MA0141.10.642
MA0142.10.601
MA0143.10.613
MA0144.10.634
MA0145.10.184
MA0146.10.401
MA0147.10.446
MA0148.10.946
MA0149.10.764
MA0150.10.137
MA0152.10.115
MA0153.10.554
MA0154.10.284
MA0155.10.546
MA0156.14.64455e-5
MA0157.10.194
MA0159.10.913
MA0160.10.599
MA0162.10.0404
MA0163.10.00655
MA0164.10.845
MA0258.10.73
MA0259.10.284



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: CNhs12569

Novel motifP-value
10.281
100.602
1000.367
1010.833
1020.115
1030.304
1040.376
1050.409
1060.0901
1070.00883
1080.372
1090.152
110.287
1100.201
1110.976
1120.38
1130.964
1140.478
1150.979
1160.0357
1170.975
1180.358
1190.983
120.555
1200.425
1210.963
1220.424
1230.00815
1240.913
1250.335
1260.774
1270.265
1280.183
1290.863
130.794
1300.302
1310.874
1320.513
1330.267
1340.263
1350.821
1360.931
1370.00769
1380.712
1390.798
140.414
1400.368
1410.622
1420.691
1430.126
1440.274
1450.59
1460.124
1470.113
1480.906
1490.0508
150.663
1500.339
1510.462
1520.021
1530.567
1540.715
1550.0655
1560.636
1570.326
1580.0946
1590.61
160.0409
1600.136
1610.776
1620.648
1630.453
1640.252
1650.231
1660.0615
1670.689
1680.491
1690.0904
170.182
180.0683
190.0448
20.381
200.743
210.309
220.204
230.653
240.502
250.222
260.513
270.516
280.383
290.926
30.443
300.342
310.197
322.66187e-8
330.281
340.581
350.748
360.638
370.0295
380.736
390.325
40.724
400.105
410.366
420.916
430.345
440.707
450.476
460.336
470.851
480.351
490.3
50.575
500.404
510.29
520.664
530.472
540.517
550.377
560.694
570.548
580.171
590.206
60.813
600.988
610.324
620.292
630.197
640.669
650.625
660.381
670.637
680.83
690.964
70.82
700.587
710.541
720.694
730.0332
740.792
750.931
760.564
770.103
780.759
790.0254
80.0705
800.283
810.734
820.972
830.288
840.311
850.14
860.821
870.203
880.369
890.185
90.71
900.625
910.479
920.15
930.8
940.131
950.0809
960.913
970.708
980.445
995.89335e-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: CNhs12569


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)
0002588 (smooth muscle cell of the umbilical vein)

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)
0001638 (vein)
0001981 (blood vessel)
0002036 (striated muscle tissue)
0002049 (vasculature)
0002050 (embryonic structure)
0002066 (umbilical vein)
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)
0003914 (epithelial tube)
0003920 (venous blood vessel)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004290 (dermomyotome)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004582 (venous 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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