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FF:11246-116E4: 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 16:36, 29 March 2012


Name:Intestinal epithelial cells (polarized), donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesmall intestine
dev stage19 years old adult
sexunknown
age19
cell typeepithelial cell, intestinal
cell lineNA
companyCell systems
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-penis0.143
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-lymphoma0.394
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: CNhs10875

Jaspar motifP-value
MA0002.20.00736
MA0003.10.433
MA0004.10.0347
MA0006.10.133
MA0007.10.65
MA0009.10.0624
MA0014.10.0132
MA0017.16.56511e-29
MA0018.20.284
MA0019.10.528
MA0024.10.00115
MA0025.10.0367
MA0027.10.655
MA0028.18.73073e-4
MA0029.10.00677
MA0030.19.20127e-4
MA0031.14.02952e-4
MA0035.21.12112e-5
MA0038.10.00367
MA0039.20.00162
MA0040.10.295
MA0041.10.495
MA0042.10.713
MA0043.10.724
MA0046.12.19185e-110
MA0047.21.37821e-10
MA0048.10.804
MA0050.10.776
MA0051.10.212
MA0052.10.0222
MA0055.10.00487
MA0057.10.912
MA0058.10.00233
MA0059.10.188
MA0060.18.29151e-13
MA0061.12.70535e-4
MA0062.20.0288
MA0065.28.47848e-8
MA0066.10.71
MA0067.10.0115
MA0068.10.81
MA0069.10.731
MA0070.10.239
MA0071.10.789
MA0072.10.689
MA0073.10.527
MA0074.10.41
MA0076.10.00258
MA0077.10.445
MA0078.10.444
MA0079.20.607
MA0080.23.72118e-8
MA0081.10.0034
MA0083.10.0501
MA0084.10.892
MA0087.10.598
MA0088.10.941
MA0090.10.00336
MA0091.10.0706
MA0092.10.162
MA0093.10.0177
MA0099.26.78306e-4
MA0100.10.422
MA0101.10.0106
MA0102.20.802
MA0103.11.07781e-9
MA0104.20.122
MA0105.10.00337
MA0106.10.331
MA0107.10.00137
MA0108.20.104
MA0111.10.738
MA0112.20.538
MA0113.10.954
MA0114.13.16727e-43
MA0115.11.07175e-8
MA0116.10.0353
MA0117.10.733
MA0119.10.0793
MA0122.10.718
MA0124.10.317
MA0125.10.0103
MA0131.10.422
MA0135.10.0275
MA0136.15.02398e-5
MA0137.20.65
MA0138.20.701
MA0139.10.0453
MA0140.10.00212
MA0141.10.00523
MA0142.10.731
MA0143.10.831
MA0144.10.803
MA0145.10.604
MA0146.10.0725
MA0147.10.511
MA0148.14.33459e-10
MA0149.10.484
MA0150.10.00173
MA0152.10.857
MA0153.14.95883e-72
MA0154.10.466
MA0155.10.956
MA0156.10.0036
MA0157.10.185
MA0159.10.0805
MA0160.10.0458
MA0162.10.331
MA0163.10.927
MA0164.10.0631
MA0258.10.802
MA0259.10.715



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: CNhs10875

Novel motifP-value
10.951
100.661
1000.172
1010.626
1020.2
1030.955
1040.615
1050.473
1060.254
1070.625
1080.827
1090.0629
110.656
1100.954
1110.65
1120.334
1130.00584
1140.427
1150.679
1160.226
1170.276
1180.207
1190.187
120.927
1200.187
1210.697
1220.326
1230.0661
1240.9
1250.0167
1260.143
1270.201
1280.0168
1290.485
130.0015
1300.782
1310.0686
1320.822
1330.238
1340.0468
1350.0538
1360.0115
1370.0122
1380.091
1390.0274
140.445
1400.809
1410.931
1420.793
1430.00233
1440.337
1450.407
1460.913
1470.762
1480.911
1490.91
150.647
1500.397
1510.633
1520.261
1530.197
1540.0236
1550.109
1560.224
1570.582
1580.973
1590.623
160.943
1600.617
1610.513
1620.956
1630.659
1640.897
1650.985
1660.193
1670.896
1680.94
1690.215
170.33
180.0294
190.976
20.977
200.512
210.277
220.789
230.342
240.577
250.984
260.436
270.956
280.965
290.233
30.506
300.392
310.988
320.149
330.55
340.638
350.412
360.536
370.88
380.463
390.509
40.561
400.0139
410.0166
420.647
430.544
440.181
450.107
460.802
470.568
480.627
490.398
50.408
500.441
510.904
520.991
530.583
540.622
550.509
560.815
570.559
580.745
590.562
60.279
600.683
610.208
620.386
630.839
640.959
650.663
660.0608
670.104
680.0548
690.446
70.0779
700.63
710.845
720.693
730.0862
740.0243
750.212
760.948
770.574
788.95925e-5
790.193
80.596
800.939
810.106
820.0643
830.717
840.227
850.183
860.527
870.204
880.676
890.476
90.184
900.958
910.0147
920.304
930.951
940.0488
950.181
960.25
970.583
980.961
990.216



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: CNhs10875


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)
0000066 (epithelial cell)
0000223 (endodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0002321 (embryonic cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)

UBERON: Anatomy
0000060 (anatomical wall)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000160 (intestine)
0000344 (mucosa)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000485 (simple columnar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001242 (intestinal mucosa)
0001262 (wall of intestine)
0001277 (intestinal epithelium)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003350 (epithelium of mucosa)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004786 (gastrointestinal system mucosa)
0004808 (gastrointestinal system epithelium)
0004921 (subdivision of digestive tract)
0004923 (organ component layer)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0007026 (primitive gut)

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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