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FF:11391-118C5: 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 17:06, 29 March 2012


Name:Smooth Muscle Cells - Brain Vascular, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stagefetus
sexunknown
agefetal
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 number4342
catalog numberSC1105
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-lymphoma-0.143
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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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: CNhs12004

Jaspar motifP-value
MA0002.20.152
MA0003.10.229
MA0004.10.642
MA0006.10.0515
MA0007.10.105
MA0009.10.295
MA0014.10.775
MA0017.10.538
MA0018.22.59631e-4
MA0019.10.831
MA0024.15.70974e-6
MA0025.10.00165
MA0027.10.296
MA0028.10.102
MA0029.10.203
MA0030.10.0877
MA0031.10.0122
MA0035.20.377
MA0038.10.805
MA0039.20.794
MA0040.10.957
MA0041.10.221
MA0042.10.421
MA0043.15.03715e-4
MA0046.10.638
MA0047.20.276
MA0048.10.515
MA0050.10.216
MA0051.10.534
MA0052.17.70665e-4
MA0055.10.439
MA0057.10.78
MA0058.10.677
MA0059.10.189
MA0060.10.0179
MA0061.10.0053
MA0062.29.55257e-6
MA0065.20.288
MA0066.10.572
MA0067.10.00865
MA0068.10.841
MA0069.10.26
MA0070.10.955
MA0071.10.285
MA0072.10.393
MA0073.10.739
MA0074.10.178
MA0076.10.0109
MA0077.10.702
MA0078.10.325
MA0079.20.4
MA0080.29.40174e-10
MA0081.10.00858
MA0083.19.1041e-4
MA0084.10.173
MA0087.10.0706
MA0088.10.63
MA0090.19.70695e-6
MA0091.10.0197
MA0092.10.233
MA0093.10.772
MA0099.20.00304
MA0100.10.171
MA0101.10.0188
MA0102.20.711
MA0103.10.00439
MA0104.20.0143
MA0105.10.0188
MA0106.10.56
MA0107.10.0131
MA0108.20.209
MA0111.10.974
MA0112.20.227
MA0113.10.403
MA0114.10.372
MA0115.10.168
MA0116.10.0537
MA0117.10.236
MA0119.10.298
MA0122.10.846
MA0124.10.502
MA0125.10.945
MA0131.10.15
MA0135.10.118
MA0136.14.22951e-13
MA0137.20.754
MA0138.20.327
MA0139.10.42
MA0140.10.638
MA0141.10.966
MA0142.10.458
MA0143.10.681
MA0144.10.194
MA0145.10.216
MA0146.10.3
MA0147.10.0119
MA0148.10.642
MA0149.10.356
MA0150.10.112
MA0152.10.86
MA0153.10.215
MA0154.10.221
MA0155.10.185
MA0156.16.61796e-8
MA0157.10.0431
MA0159.10.314
MA0160.10.353
MA0162.10.0227
MA0163.10.746
MA0164.10.619
MA0258.10.724
MA0259.10.113



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: CNhs12004

Novel motifP-value
10.32
100.221
1000.701
1010.452
1020.0619
1030.628
1040.575
1050.158
1060.451
1070.128
1080.365
1090.619
110.992
1100.895
1110.129
1120.349
1130.649
1140.654
1150.145
1160.033
1170.54
1180.299
1190.742
120.189
1200.363
1210.67
1220.0175
1230.0102
1240.289
1250.0584
1260.976
1270.758
1280.22
1290.334
130.321
1300.446
1310.935
1320.445
1330.494
1340.439
1350.254
1360.234
1370.0261
1380.891
1390.512
140.209
1400.338
1410.128
1420.743
1430.46
1440.51
1450.394
1460.799
1470.109
1480.64
1490.315
150.544
1500.413
1510.358
1520.0286
1530.568
1540.415
1550.00645
1560.3
1570.384
1580.0114
1590.405
160.077
1600.781
1610.806
1620.358
1630.131
1640.299
1650.0491
1660.231
1670.511
1680.103
1690.225
170.86
180.958
190.253
20.431
200.34
210.88
220.249
230.37
240.46
250.0384
260.312
270.505
280.194
290.779
30.948
300.38
310.366
322.96932e-18
330.849
340.513
350.145
360.0378
370.684
380.372
390.586
40.0694
400.286
410.0824
420.353
430.56
440.282
450.94
460.718
470.728
480.852
490.103
50.614
500.834
510.521
520.723
530.152
540.66
550.245
560.788
570.896
580.0246
590.699
60.569
600.462
610.938
620.0655
630.938
640.542
650.831
660.904
670.273
680.864
690.667
70.215
700.322
710.505
720.975
730.0243
740.834
750.116
760.494
770.245
780.961
790.0801
80.373
800.135
810.868
820.813
830.92
840.855
850.458
860.964
870.0272
880.997
890.693
90.791
900.38
910.776
920.158
930.118
940.619
950.442
960.389
970.418
980.0872
992.03874e-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: CNhs12004


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)
0002590 (smooth muscle cell of the brain vasculature)

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000119 (cell layer)
0000153 (anterior region of body)
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)
0000924 (ectoderm)
0000926 (mesoderm)
0000955 (brain)
0001009 (circulatory system)
0001015 (musculature)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0002036 (striated muscle tissue)
0002049 (vasculature)
0002050 (embryonic structure)
0002200 (vasculature of head)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004290 (dermomyotome)
0004535 (cardiovascular system)
0005284 (brain vasculature)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
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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