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FF:11239-116D6: 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 - Colonic, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecolon
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 number1830
catalog numberSC2945
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-0.0868
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-lymphoma0.166
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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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: CNhs10868

Jaspar motifP-value
MA0002.20.00269
MA0003.10.776
MA0004.10.679
MA0006.10.418
MA0007.10.41
MA0009.10.304
MA0014.10.696
MA0017.10.222
MA0018.29.26715e-5
MA0019.10.161
MA0024.10.771
MA0025.11.95946e-4
MA0027.10.757
MA0028.10.659
MA0029.10.804
MA0030.10.0781
MA0031.10.347
MA0035.20.00972
MA0038.10.207
MA0039.20.228
MA0040.10.659
MA0041.10.105
MA0042.10.646
MA0043.10.00793
MA0046.10.376
MA0047.20.226
MA0048.10.208
MA0050.10.021
MA0051.10.034
MA0052.10.208
MA0055.10.264
MA0057.10.689
MA0058.10.904
MA0059.10.638
MA0060.10.475
MA0061.10.0024
MA0062.21.58017e-4
MA0065.20.137
MA0066.10.83
MA0067.10.0159
MA0068.17.15654e-4
MA0069.10.097
MA0070.10.589
MA0071.10.926
MA0072.10.307
MA0073.10.239
MA0074.10.875
MA0076.10.518
MA0077.10.472
MA0078.10.692
MA0079.20.0489
MA0080.23.13248e-11
MA0081.10.057
MA0083.10.0335
MA0084.10.0816
MA0087.10.412
MA0088.10.067
MA0090.12.87045e-6
MA0091.10.00152
MA0092.10.426
MA0093.10.806
MA0099.22.66897e-5
MA0100.10.759
MA0101.10.00637
MA0102.20.804
MA0103.16.39308e-6
MA0104.20.14
MA0105.10.53
MA0106.10.0233
MA0107.10.00128
MA0108.20.0702
MA0111.10.592
MA0112.20.361
MA0113.10.531
MA0114.10.601
MA0115.10.118
MA0116.10.87
MA0117.10.707
MA0119.10.0464
MA0122.10.277
MA0124.10.604
MA0125.10.39
MA0131.10.949
MA0135.10.0158
MA0136.14.70415e-11
MA0137.20.714
MA0138.20.163
MA0139.10.513
MA0140.10.422
MA0141.10.343
MA0142.10.0512
MA0143.10.859
MA0144.10.578
MA0145.10.248
MA0146.10.525
MA0147.10.0695
MA0148.10.408
MA0149.10.448
MA0150.10.00283
MA0152.10.00579
MA0153.10.325
MA0154.10.338
MA0155.10.98
MA0156.11.67901e-8
MA0157.10.465
MA0159.10.142
MA0160.10.0333
MA0162.10.028
MA0163.10.244
MA0164.10.761
MA0258.10.53
MA0259.10.439



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: CNhs10868

Novel motifP-value
10.502
100.887
1000.0559
1010.552
1020.00264
1030.647
1040.815
1050.933
1060.151
1070.462
1080.478
1090.348
110.76
1100.369
1110.314
1120.617
1130.894
1140.536
1150.773
1160.173
1170.323
1180.466
1190.283
120.168
1200.54
1210.72
1220.00325
1230.0142
1240.553
1250.751
1260.732
1270.115
1280.709
1290.348
130.509
1300.0318
1310.44
1320.715
1330.583
1340.972
1350.93
1360.754
1370.023
1380.602
1390.0724
140.19
1400.357
1410.68
1420.235
1430.229
1440.378
1450.744
1460.387
1470.151
1480.8
1490.321
150.0911
1500.885
1510.719
1520.869
1530.639
1540.385
1558.1771e-5
1560.458
1570.222
1580.00634
1590.24
160.451
1600.772
1610.657
1620.257
1630.575
1640.786
1650.449
1660.0154
1670.351
1680.187
1690.384
170.616
180.538
190.0195
20.898
200.426
210.563
220.937
230.813
240.731
250.146
260.658
270.665
280.202
290.895
30.657
300.729
310.937
323.54749e-9
330.637
340.972
350.268
360.206
370.693
380.297
390.478
40.0518
400.416
410.008
420.585
430.469
440.505
450.198
460.582
470.542
480.529
490.119
50.68
500.557
511
520.789
530.215
540.809
550.201
560.76
570.917
580.127
590.199
60.768
600.079
610.384
620.161
630.946
640.569
650.639
660.351
670.852
680.466
690.445
70.306
700.00794
710.244
720.333
730.469
740.117
750.437
760.853
770.52
780.211
790.25
80.621
800.132
810.855
820.347
830.721
840.338
850.232
860.904
870.813
880.469
890.713
90.892
900.589
910.676
920.499
930.54
940.389
950.782
960.292
970.584
980.0643
994.22916e-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: CNhs10868


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)
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)
0002504 (enteric smooth muscle cell)
1000280 (smooth muscle cell of colon)

UBERON: Anatomy
0000059 (large intestine)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000119 (cell layer)
0000160 (intestine)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001007 (digestive system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001135 (smooth muscle tissue)
0001155 (colon)
0001555 (digestive tract)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004290 (dermomyotome)
0004921 (subdivision of digestive tract)
0005291 (embryonic tissue)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)
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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