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FF:11257-116F6: 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 17:01, 29 March 2012


Name:Smooth Muscle Cells - Prostate, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueprostate
dev stage40 years old adult
sexmale
age40
cell typesmooth muscle cell
cell lineNA
companyLonza
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-0.0721
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-lymphoma0.226
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: CNhs11920

Jaspar motifP-value
MA0002.20.00104
MA0003.10.373
MA0004.10.0159
MA0006.10.516
MA0007.10.883
MA0009.10.696
MA0014.10.312
MA0017.10.314
MA0018.27.20534e-5
MA0019.10.986
MA0024.10.507
MA0025.10.0555
MA0027.10.681
MA0028.10.0777
MA0029.10.735
MA0030.10.587
MA0031.10.518
MA0035.20.437
MA0038.10.11
MA0039.20.148
MA0040.10.347
MA0041.10.879
MA0042.10.919
MA0043.10.0165
MA0046.10.803
MA0047.20.242
MA0048.10.226
MA0050.10.284
MA0051.10.518
MA0052.10.259
MA0055.10.618
MA0057.10.234
MA0058.10.00655
MA0059.10.0293
MA0060.10.581
MA0061.10.0548
MA0062.20.281
MA0065.20.13
MA0066.10.749
MA0067.10.0108
MA0068.10.0817
MA0069.10.138
MA0070.10.283
MA0071.10.952
MA0072.10.837
MA0073.10.251
MA0074.10.471
MA0076.10.133
MA0077.10.38
MA0078.10.303
MA0079.20.417
MA0080.22.77414e-9
MA0081.10.01
MA0083.10.00507
MA0084.10.0939
MA0087.10.775
MA0088.10.53
MA0090.10.00174
MA0091.10.00754
MA0092.10.871
MA0093.10.0315
MA0099.20.0106
MA0100.10.464
MA0101.10.0401
MA0102.20.399
MA0103.14.92025e-4
MA0104.24.28323e-4
MA0105.10.395
MA0106.10.507
MA0107.10.0237
MA0108.20.13
MA0111.10.244
MA0112.20.561
MA0113.10.954
MA0114.10.448
MA0115.10.199
MA0116.10.411
MA0117.10.408
MA0119.10.693
MA0122.10.25
MA0124.10.944
MA0125.10.177
MA0131.10.524
MA0135.10.812
MA0136.14.94691e-10
MA0137.20.602
MA0138.20.131
MA0139.10.517
MA0140.10.689
MA0141.10.273
MA0142.10.0113
MA0143.10.412
MA0144.10.938
MA0145.10.878
MA0146.10.207
MA0147.10.00204
MA0148.10.319
MA0149.10.27
MA0150.10.0111
MA0152.10.0366
MA0153.10.885
MA0154.10.873
MA0155.10.894
MA0156.18.92765e-5
MA0157.10.259
MA0159.10.543
MA0160.10.0977
MA0162.10.0852
MA0163.10.0788
MA0164.10.557
MA0258.10.114
MA0259.10.314



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: CNhs11920

Novel motifP-value
10.243
100.828
1000.65
1010.367
1020.194
1030.673
1040.889
1050.537
1060.0469
1070.968
1080.74
1090.73
110.698
1100.42
1110.0976
1120.783
1130.189
1140.112
1150.628
1160.764
1170.827
1180.521
1190.427
120.35
1200.588
1210.983
1220.0287
1230.00781
1240.976
1250.132
1260.688
1270.943
1280.24
1290.194
130.452
1300.0537
1310.586
1320.224
1330.818
1340.182
1350.641
1360.696
1370.111
1380.172
1390.0403
140.18
1400.367
1410.226
1420.826
1430.482
1440.824
1450.272
1460.381
1470.173
1480.771
1490.223
150.0356
1500.917
1510.354
1520.432
1530.685
1540.181
1550.0521
1560.597
1570.413
1580.0498
1590.594
160.929
1600.694
1610.316
1620.689
1630.979
1640.643
1650.14
1660.135
1670.516
1680.972
1690.178
170.688
180.741
190.0322
20.248
200.431
210.378
220.308
230.757
240.601
250.327
260.272
270.641
280.222
290.881
30.739
300.225
310.85
325.77066e-6
331
340.896
350.435
360.166
370.696
380.171
390.478
40.0328
400.568
410.0401
420.479
430.314
440.581
450.938
460.605
470.437
480.429
490.113
50.292
500.417
510.952
520.5
530.29
540.923
550.768
560.667
570.365
580.237
590.638
60.355
600.127
610.954
620.405
630.693
640.445
650.535
660.531
670.728
680.821
690.754
70.167
700.0284
710.872
720.523
730.265
740.734
750.873
760.228
770.468
780.025
790.138
80.862
800.617
810.191
820.627
830.132
840.955
850.144
860.877
870.568
880.652
890.615
90.698
900.318
910.635
920.596
930.519
940.62
950.688
960.215
970.517
980.0524
990.0275



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: CNhs11920


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)
1000487 (smooth muscle cell of prostate)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000079 (male reproductive system)
0000119 (cell layer)
0000161 (orifice)
0000162 (cloaca)
0000163 (embryonic cloaca)
0000164 (primitive urogenital sinus)
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)
0000925 (endoderm)
0000926 (mesoderm)
0000990 (reproductive system)
0001007 (digestive system)
0001015 (musculature)
0001046 (hindgut)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001353 (anal region)
0001555 (digestive tract)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002367 (prostate gland)
0002385 (muscle tissue)
0002530 (gland)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003064 (intermediate mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003101 (male organism)
0003104 (mesenchyme)
0003353 (epithelium of hindgut)
0003820 (prostate bud)
0003929 (gut epithelium)
0003937 (sex gland)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004122 (genitourinary system)
0004185 (endodermal part of digestive tract)
0004290 (dermomyotome)
0004902 (urogenital sinus epithelium)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005156 (reproductive structure)
0005291 (embryonic tissue)
0005399 (male reproductive gland)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006866 (terminal part of digestive tract)
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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