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FF:11234-116D1: 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 16:35, 29 March 2012


Name:Smooth Muscle Cells - Brain Vascular, donor1
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 number2733
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-0.148
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-lymphoma0.182
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: CNhs10863

Jaspar motifP-value
MA0002.20.209
MA0003.10.49
MA0004.10.544
MA0006.10.123
MA0007.10.531
MA0009.10.174
MA0014.10.469
MA0017.10.524
MA0018.20.0034
MA0019.10.485
MA0024.10.0863
MA0025.11.0718e-4
MA0027.10.705
MA0028.10.0725
MA0029.10.548
MA0030.10.0178
MA0031.10.00508
MA0035.20.0417
MA0038.10.00369
MA0039.20.162
MA0040.10.807
MA0041.10.96
MA0042.10.407
MA0043.10.00324
MA0046.10.883
MA0047.20.357
MA0048.10.165
MA0050.10.712
MA0051.10.589
MA0052.10.71
MA0055.10.191
MA0057.10.868
MA0058.10.252
MA0059.10.393
MA0060.14.85049e-4
MA0061.11.81579e-5
MA0062.20.0204
MA0065.20.589
MA0066.10.544
MA0067.10.0503
MA0068.10.283
MA0069.10.948
MA0070.10.526
MA0071.10.878
MA0072.10.733
MA0073.10.999
MA0074.10.329
MA0076.10.583
MA0077.10.697
MA0078.10.195
MA0079.20.23
MA0080.21.25486e-9
MA0081.10.189
MA0083.10.0113
MA0084.10.184
MA0087.10.0273
MA0088.10.476
MA0090.11.14455e-5
MA0091.10.0984
MA0092.10.812
MA0093.10.535
MA0099.24.46647e-4
MA0100.10.481
MA0101.11.4519e-4
MA0102.20.00584
MA0103.11.35493e-4
MA0104.20.142
MA0105.10.051
MA0106.10.618
MA0107.11.51795e-5
MA0108.20.328
MA0111.10.52
MA0112.20.628
MA0113.10.822
MA0114.10.965
MA0115.10.438
MA0116.10.848
MA0117.10.561
MA0119.10.178
MA0122.10.612
MA0124.10.17
MA0125.10.525
MA0131.10.368
MA0135.10.443
MA0136.13.13097e-10
MA0137.20.916
MA0138.20.416
MA0139.10.992
MA0140.10.975
MA0141.10.993
MA0142.10.347
MA0143.10.552
MA0144.10.811
MA0145.10.85
MA0146.10.373
MA0147.10.0491
MA0148.10.592
MA0149.10.875
MA0150.17.71801e-4
MA0152.10.00942
MA0153.10.0837
MA0154.10.0409
MA0155.10.997
MA0156.15.66278e-5
MA0157.10.125
MA0159.10.0279
MA0160.10.0886
MA0162.10.019
MA0163.10.761
MA0164.10.247
MA0258.10.108
MA0259.10.864



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: CNhs10863

Novel motifP-value
10.445
100.871
1000.63
1010.832
1020.00608
1030.871
1040.917
1050.881
1060.0487
1070.286
1080.152
1090.867
110.894
1100.37
1110.288
1120.246
1130.382
1140.985
1150.504
1160.198
1170.774
1180.179
1190.82
120.158
1200.981
1210.94
1220.00563
1239.16613e-4
1240.708
1250.903
1260.673
1270.152
1280.655
1290.889
130.683
1300.0107
1310.08
1320.322
1330.121
1340.0471
1350.185
1360.672
1370.0161
1380.197
1390.0918
140.284
1400.129
1410.0477
1420.431
1430.196
1440.584
1450.518
1460.0536
1470.324
1480.154
1490.585
150.241
1500.554
1510.457
1520.748
1530.748
1540.164
1550.0038
1560.239
1570.197
1580.00635
1590.0691
160.752
1600.971
1610.821
1620.244
1630.96
1640.0326
1650.548
1660.111
1670.992
1680.37
1690.318
170.992
180.691
190.0693
20.933
200.656
210.954
220.39
230.317
240.546
250.258
260.443
270.707
280.118
290.477
30.709
300.21
310.693
322.17427e-5
330.147
340.785
350.29
360.813
370.507
380.399
390.336
40.0128
400.792
410.0235
420.931
430.166
440.861
450.304
460.148
470.816
480.94
490.0399
50.729
500.619
510.477
520.858
530.056
540.91
550.787
560.909
570.772
580.0419
590.648
60.908
600.0637
610.804
620.0487
630.537
640.454
650.748
660.202
670.663
680.171
690.866
70.616
700.155
710.569
720.423
730.507
740.495
750.624
760.85
770.759
780.922
790.397
80.411
800.886
810.718
820.0463
830.412
840.969
850.821
860.483
870.336
880.691
890.602
90.994
900.726
910.969
920.151
930.818
940.423
950.889
960.212
970.306
980.737
992.94251e-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: CNhs10863


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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