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FF:11315-117D1: 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 17:00, 29 March 2012


Name:Smooth Muscle Cells - Brain Vascular, donor2
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 number4731
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-penis-0.104
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-lymphoma0.214
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11900

Jaspar motifP-value
MA0002.20.0772
MA0003.10.902
MA0004.10.716
MA0006.10.212
MA0007.10.572
MA0009.10.00508
MA0014.10.673
MA0017.10.213
MA0018.20.019
MA0019.10.911
MA0024.10.715
MA0025.10.00847
MA0027.10.299
MA0028.10.833
MA0029.10.272
MA0030.10.17
MA0031.10.019
MA0035.20.113
MA0038.10.00487
MA0039.20.39
MA0040.10.786
MA0041.10.988
MA0042.10.752
MA0043.13.78592e-4
MA0046.10.482
MA0047.20.182
MA0048.10.247
MA0050.10.132
MA0051.10.952
MA0052.10.0221
MA0055.10.501
MA0057.10.933
MA0058.10.964
MA0059.10.136
MA0060.10.0334
MA0061.12.5323e-6
MA0062.20.0141
MA0065.20.0163
MA0066.10.662
MA0067.10.00363
MA0068.10.384
MA0069.10.627
MA0070.10.768
MA0071.10.354
MA0072.10.4
MA0073.10.693
MA0074.10.234
MA0076.10.953
MA0077.10.786
MA0078.10.519
MA0079.20.419
MA0080.21.43177e-9
MA0081.10.0361
MA0083.11.61932e-9
MA0084.10.429
MA0087.10.456
MA0088.10.476
MA0090.15.82482e-7
MA0091.10.177
MA0092.10.616
MA0093.10.928
MA0099.20.13
MA0100.10.298
MA0101.11.55921e-4
MA0102.20.00193
MA0103.18.81785e-4
MA0104.20.0907
MA0105.12.98643e-5
MA0106.10.991
MA0107.11.89255e-5
MA0108.20.068
MA0111.10.365
MA0112.20.322
MA0113.10.814
MA0114.10.0807
MA0115.10.00766
MA0116.10.0179
MA0117.10.445
MA0119.10.366
MA0122.10.971
MA0124.10.161
MA0125.10.668
MA0131.10.919
MA0135.10.704
MA0136.19.01084e-9
MA0137.20.827
MA0138.20.239
MA0139.10.571
MA0140.10.918
MA0141.10.0123
MA0142.10.655
MA0143.10.878
MA0144.10.659
MA0145.10.627
MA0146.10.481
MA0147.10.045
MA0148.10.251
MA0149.10.436
MA0150.10.0284
MA0152.10.188
MA0153.10.0266
MA0154.10.0169
MA0155.10.784
MA0156.14.27567e-6
MA0157.10.275
MA0159.10.0906
MA0160.10.00165
MA0162.10.0852
MA0163.10.324
MA0164.10.425
MA0258.10.0133
MA0259.10.371



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: CNhs11900

Novel motifP-value
10.069
100.216
1000.748
1010.874
1020.0375
1030.475
1040.909
1050.469
1060.0245
1070.291
1080.0642
1090.299
110.441
1100.698
1110.031
1120.167
1130.513
1140.321
1150.322
1160.476
1170.384
1180.294
1190.789
120.0539
1200.778
1210.543
1220.108
1232.80521e-4
1240.901
1250.421
1260.502
1270.0856
1280.373
1290.878
130.304
1300.095
1310.151
1320.752
1330.042
1340.28
1350.506
1360.63
1370.0361
1380.111
1390.0821
140.375
1400.0739
1410.0249
1420.969
1430.134
1440.964
1450.619
1460.145
1470.196
1480.13
1490.377
150.474
1500.375
1510.398
1520.432
1530.494
1540.393
1555.49405e-4
1560.319
1570.0304
1580.011
1590.292
160.784
1600.481
1610.619
1620.393
1630.497
1640.288
1650.433
1660.079
1670.636
1680.388
1690.483
170.532
180.397
190.678
20.538
200.28
210.186
220.713
230.922
240.344
250.605
260.593
270.605
280.48
290.771
30.646
300.21
310.82
327.50093e-5
330.418
340.911
350.0328
360.374
370.468
380.344
390.607
40.15
400.386
410.0633
420.468
430.246
440.386
450.866
460.299
470.374
480.449
490.0864
50.784
500.677
510.433
520.718
530.224
540.966
550.373
560.563
570.974
580.0298
590.376
60.833
600.0616
610.475
620.052
630.184
640.324
650.415
660.186
670.778
680.377
690.891
70.527
700.0106
710.355
720.63
730.963
740.895
750.0434
760.35
770.387
780.51
790.663
80.847
800.655
810.612
820.0188
830.591
840.438
850.147
860.65
870.758
880.663
890.617
90.713
900.761
910.82
920.684
930.587
940.301
950.16
960.37
970.161
980.00735
990.00146



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: CNhs11900


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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