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FF:11396-118D1: 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 17:06, 29 March 2012


Name:Smooth Muscle Cells - Colonic, donor3
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 number1147
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-0.0199
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-lymphoma0.279
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs12007

Jaspar motifP-value
MA0002.20.012
MA0003.10.657
MA0004.10.963
MA0006.10.399
MA0007.10.421
MA0009.10.12
MA0014.10.722
MA0017.10.269
MA0018.20.015
MA0019.10.136
MA0024.10.0582
MA0025.10.0141
MA0027.10.947
MA0028.10.234
MA0029.10.931
MA0030.10.088
MA0031.10.0189
MA0035.20.0736
MA0038.10.104
MA0039.20.2
MA0040.10.729
MA0041.10.626
MA0042.10.491
MA0043.10.054
MA0046.10.443
MA0047.20.0358
MA0048.10.0171
MA0050.11.01529e-4
MA0051.13.48145e-4
MA0052.10.00881
MA0055.10.0295
MA0057.10.822
MA0058.10.998
MA0059.10.775
MA0060.10.00165
MA0061.11.45858e-5
MA0062.20.0648
MA0065.20.18
MA0066.10.612
MA0067.10.0168
MA0068.10.121
MA0069.10.169
MA0070.10.388
MA0071.10.586
MA0072.10.213
MA0073.10.528
MA0074.10.456
MA0076.10.706
MA0077.10.472
MA0078.10.832
MA0079.20.606
MA0080.26.50224e-13
MA0081.10.0319
MA0083.10.0383
MA0084.10.332
MA0087.10.726
MA0088.10.0651
MA0090.10.00378
MA0091.10.0447
MA0092.10.936
MA0093.10.845
MA0099.26.64118e-6
MA0100.10.75
MA0101.10.00318
MA0102.20.224
MA0103.11.81982e-4
MA0104.20.175
MA0105.17.24419e-4
MA0106.10.0144
MA0107.11.47627e-4
MA0108.20.0928
MA0111.10.869
MA0112.20.644
MA0113.10.924
MA0114.10.444
MA0115.10.296
MA0116.10.126
MA0117.10.487
MA0119.10.718
MA0122.10.0942
MA0124.10.345
MA0125.10.314
MA0131.10.988
MA0135.10.24
MA0136.15.34058e-12
MA0137.20.395
MA0138.20.434
MA0139.10.277
MA0140.10.534
MA0141.10.7
MA0142.10.164
MA0143.10.639
MA0144.10.295
MA0145.10.958
MA0146.10.487
MA0147.10.145
MA0148.10.0844
MA0149.10.352
MA0150.10.00226
MA0152.10.0912
MA0153.10.313
MA0154.10.0461
MA0155.10.817
MA0156.14.00235e-7
MA0157.10.0452
MA0159.10.0225
MA0160.10.186
MA0162.10.0401
MA0163.10.32
MA0164.10.76
MA0258.10.196
MA0259.10.596



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: CNhs12007

Novel motifP-value
10.338
100.977
1000.156
1010.43
1020.156
1030.745
1040.863
1050.169
1060.134
1070.911
1080.614
1090.418
110.742
1100.476
1110.38
1120.218
1130.13
1140.217
1150.125
1160.16
1170.612
1180.995
1190.117
120.266
1200.204
1210.345
1220.019
1230.0476
1240.0641
1250.265
1260.753
1270.233
1280.706
1290.0455
130.861
1300.0137
1310.577
1320.948
1330.913
1340.446
1350.386
1360.0863
1370.0226
1380.121
1390.113
140.126
1400.227
1410.318
1420.899
1430.343
1440.827
1450.544
1460.802
1470.438
1480.279
1490.803
150.0703
1500.768
1510.919
1520.138
1530.389
1540.819
1555.98858e-4
1560.517
1570.409
1580.00944
1590.177
160.634
1600.911
1610.731
1620.238
1630.947
1640.285
1650.42
1660.0385
1670.321
1680.0929
1690.616
170.605
180.644
190.436
20.905
200.74
210.586
220.83
230.203
240.584
250.14
260.418
270.703
280.166
290.743
30.656
300.617
310.92
325.89085e-11
330.971
340.989
350.418
360.0543
370.893
380.385
390.658
40.145
400.685
410.0073
420.329
430.274
440.659
450.185
460.323
470.607
480.66
490.107
50.181
500.672
510.83
520.604
530.125
540.688
550.58
560.761
570.484
580.0859
590.537
60.632
600.15
610.906
620.055
630.625
640.572
650.525
660.611
670.86
680.83
690.709
70.216
700.00106
710.908
720.457
730.123
740.0717
750.42
760.55
770.777
780.271
790.0504
80.809
800.0528
810.486
820.121
830.987
840.622
850.285
860.578
870.0809
880.532
890.646
90.91
900.576
910.513
920.288
930.0751
940.51
950.257
960.061
970.905
980.174
996.63608e-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: CNhs12007


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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