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{{f5samples
{{f5samples
|F5samples=
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000144,CL:0000220,CL:0000223,CL:0000255,CL:0000548,CL:0002076,CL:0002251,CL:0002321,CL:0002371,CL:0002563
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000144,CL:0000220,CL:0000223,CL:0000255,CL:0000548,CL:0002076,CL:0002251,CL:0002321,CL:0002371,CL:0002563
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100003
|fonse_cell_line=FF:0100003
|fonse_cell_line_closure=FF:0100003
|fonse_cell_line_closure=FF:0100003

Revision as of 17:02, 29 March 2012


Name:normal intestinal epithelial cell line:FHs 74 Int
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 stageNA
sexfemale
agefetal
cell typeepithelial cell, intestinal
cell lineFHs 74 Int
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
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-penis0.003
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-lymphoma-0.109
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: CNhs11950

Jaspar motifP-value
MA0002.20.395
MA0003.10.251
MA0004.10.0273
MA0006.10.088
MA0007.10.52
MA0009.10.958
MA0014.10.724
MA0017.10.927
MA0018.23.39501e-7
MA0019.10.644
MA0024.10.00654
MA0025.18.20993e-4
MA0027.10.885
MA0028.10.00323
MA0029.10.503
MA0030.10.426
MA0031.10.0892
MA0035.20.555
MA0038.10.119
MA0039.20.0416
MA0040.10.201
MA0041.10.968
MA0042.10.229
MA0043.11.50361e-6
MA0046.10.393
MA0047.20.751
MA0048.10.351
MA0050.12.705e-8
MA0051.15.02121e-6
MA0052.10.503
MA0055.10.162
MA0057.10.0926
MA0058.10.00111
MA0059.10.461
MA0060.12.13449e-9
MA0061.10.381
MA0062.25.10221e-9
MA0065.20.147
MA0066.10.354
MA0067.10.00519
MA0068.10.736
MA0069.10.294
MA0070.10.372
MA0071.10.397
MA0072.10.823
MA0073.10.804
MA0074.10.255
MA0076.11.97872e-4
MA0077.10.645
MA0078.10.913
MA0079.20.89
MA0080.24.62472e-8
MA0081.10.0213
MA0083.10.123
MA0084.10.749
MA0087.10.953
MA0088.10.513
MA0090.10.00432
MA0091.10.00346
MA0092.10.452
MA0093.10.0169
MA0099.22.65772e-6
MA0100.10.0758
MA0101.10.0101
MA0102.20.391
MA0103.10.0718
MA0104.20.00536
MA0105.10.646
MA0106.10.294
MA0107.10.0663
MA0108.20.585
MA0111.10.987
MA0112.20.00943
MA0113.10.914
MA0114.10.688
MA0115.10.238
MA0116.10.0506
MA0117.10.107
MA0119.10.0266
MA0122.10.334
MA0124.10.0127
MA0125.10.0511
MA0131.10.0908
MA0135.10.0216
MA0136.12.45155e-12
MA0137.20.735
MA0138.20.276
MA0139.10.581
MA0140.10.545
MA0141.10.259
MA0142.10.785
MA0143.10.496
MA0144.10.705
MA0145.10.103
MA0146.10.566
MA0147.10.0271
MA0148.10.993
MA0149.10.483
MA0150.10.0142
MA0152.10.981
MA0153.10.922
MA0154.10.206
MA0155.10.109
MA0156.11.13956e-9
MA0157.10.249
MA0159.10.276
MA0160.10.816
MA0162.10.034
MA0163.10.00571
MA0164.10.794
MA0258.10.0211
MA0259.10.0623



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: CNhs11950

Novel motifP-value
10.983
100.872
1000.249
1010.249
1020.316
1030.203
1040.679
1050.102
1060.0192
1070.013
1080.207
1090.0736
110.352
1100.38
1110.766
1120.219
1130.555
1140.196
1150.0014
1160.0188
1170.637
1180.547
1190.239
120.265
1200.338
1210.0674
1220.0369
1230.362
1240.477
1250.86
1260.958
1270.994
1280.0295
1290.139
130.77
1300.708
1310.676
1320.37
1330.922
1340.829
1350.675
1360.229
1370.09
1380.952
1390.577
140.236
1400.86
1410.82
1420.759
1430.959
1440.552
1450.444
1460.72
1470.23
1480.419
1490.0216
150.504
1500.314
1510.411
1520.00342
1530.372
1540.542
1550.0795
1560.694
1570.264
1580.00486
1590.648
160.0471
1600.799
1610.935
1620.661
1630.304
1640.0867
1650.468
1660.0236
1670.893
1680.898
1690.0379
170.471
180.355
190.02
20.26
200.184
210.123
220.438
230.267
240.844
250.495
260.191
270.249
280.194
290.39
30.404
300.506
310.463
321.19795e-14
330.591
340.697
350.507
360.105
370.175
380.72
390.478
40.289
400.733
410.293
420.761
430.217
440.015
450.711
460.265
470.478
480.962
490.943
50.875
500.502
510.45
520.604
530.313
540.603
550.253
560.718
570.533
580.812
590.0101
60.871
600.796
610.419
620.494
630.375
640.915
650.412
660.184
670.503
680.598
690.344
70.483
700.125
710.104
720.637
730.00444
740.734
750.818
760.847
770.0183
780.439
797.9524e-4
80.0945
800.0705
810.537
820.201
830.811
840.913
850.0216
860.656
870.266
880.9
890.165
90.46
900.664
910.5
920.356
930.0842
940.644
950.0428
960.918
970.773
980.744
993.39551e-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: CNhs11950


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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