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FF:11320-117D6: 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 17:03, 29 March 2012


Name:Smooth Muscle Cells - Colonic, donor2
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 number1151
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-0.0405
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-lymphoma0.143
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: CNhs11963

Jaspar motifP-value
MA0002.20.0362
MA0003.10.478
MA0004.10.299
MA0006.10.139
MA0007.10.138
MA0009.10.234
MA0014.10.517
MA0017.10.355
MA0018.23.1874e-4
MA0019.10.281
MA0024.10.884
MA0025.18.87536e-5
MA0027.10.995
MA0028.10.646
MA0029.10.906
MA0030.10.112
MA0031.10.0192
MA0035.20.245
MA0038.10.914
MA0039.20.0272
MA0040.10.481
MA0041.10.25
MA0042.10.563
MA0043.19.05615e-4
MA0046.10.424
MA0047.20.00698
MA0048.10.0773
MA0050.12.15449e-4
MA0051.13.73097e-4
MA0052.10.00236
MA0055.10.116
MA0057.10.957
MA0058.10.333
MA0059.10.741
MA0060.10.804
MA0061.14.79643e-4
MA0062.22.93394e-6
MA0065.20.686
MA0066.10.348
MA0067.11.78015e-4
MA0068.10.239
MA0069.10.221
MA0070.10.903
MA0071.10.211
MA0072.10.404
MA0073.10.52
MA0074.10.363
MA0076.10.0695
MA0077.10.335
MA0078.10.754
MA0079.20.268
MA0080.25.50059e-12
MA0081.10.00585
MA0083.10.0856
MA0084.10.273
MA0087.10.856
MA0088.10.0891
MA0090.10.0119
MA0091.10.00499
MA0092.10.7
MA0093.10.424
MA0099.25.9181e-10
MA0100.10.55
MA0101.12.14932e-5
MA0102.20.126
MA0103.15.65411e-4
MA0104.20.0322
MA0105.10.77
MA0106.10.0104
MA0107.19.87406e-7
MA0108.20.786
MA0111.10.815
MA0112.20.0285
MA0113.10.634
MA0114.10.587
MA0115.10.172
MA0116.10.166
MA0117.10.385
MA0119.10.128
MA0122.10.035
MA0124.10.116
MA0125.10.691
MA0131.10.71
MA0135.10.054
MA0136.16.32056e-15
MA0137.20.12
MA0138.20.794
MA0139.10.912
MA0140.10.552
MA0141.10.839
MA0142.10.408
MA0143.10.804
MA0144.10.133
MA0145.10.234
MA0146.10.296
MA0147.10.05
MA0148.10.134
MA0149.10.534
MA0150.12.05066e-4
MA0152.10.0463
MA0153.10.378
MA0154.10.722
MA0155.10.217
MA0156.11.36552e-12
MA0157.10.0355
MA0159.10.344
MA0160.10.194
MA0162.10.0318
MA0163.10.0019
MA0164.10.756
MA0258.10.135
MA0259.10.195



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: CNhs11963

Novel motifP-value
10.961
100.587
1000.164
1010.418
1020.0575
1030.943
1040.917
1050.0502
1060.685
1070.506
1080.877
1090.375
110.669
1100.0767
1110.524
1120.943
1130.0881
1140.938
1150.00354
1160.0155
1170.968
1180.987
1190.402
120.279
1200.158
1210.0818
1220.00824
1230.22
1240.291
1250.284
1260.801
1270.138
1280.371
1290.1
130.629
1300.108
1310.928
1320.692
1330.275
1340.42
1350.558
1360.203
1370.0271
1380.523
1390.356
140.151
1400.924
1410.968
1420.694
1430.376
1440.528
1450.658
1460.821
1470.207
1480.813
1490.133
150.183
1500.504
1510.573
1520.276
1530.826
1540.937
1553.50299e-4
1560.265
1570.921
1580.0057
1590.214
160.123
1600.46
1610.523
1620.106
1630.556
1640.119
1650.955
1660.0239
1670.495
1680.0454
1690.18
170.89
180.884
190.0197
20.27
200.374
210.207
220.542
230.862
240.925
250.19
260.399
270.947
280.174
290.401
30.655
300.591
310.537
326.10396e-20
330.916
340.714
350.524
360.0485
370.649
380.248
390.486
40.198
400.538
410.0271
420.465
430.894
440.236
450.254
460.751
470.989
480.999
490.214
50.75
500.696
510.761
520.72
530.162
540.936
550.968
560.981
570.687
580.205
590.308
60.619
600.358
610.615
620.347
630.902
640.806
650.912
660.755
670.906
680.826
690.509
70.615
700.0192
710.0548
720.28
730.138
740.042
750.78
760.89
770.461
780.223
790.00179
80.245
800.0456
810.95
820.877
830.505
840.683
850.845
860.254
870.128
880.526
890.628
90.922
900.733
910.941
920.848
930.0311
940.748
950.351
960.135
970.868
980.116
995.46138e-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: CNhs11963


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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