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FF:11527-119I6: 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 16:46, 29 March 2012


Name:Keratocytes, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueeye
dev stageNA
sexNA
ageNA
cell typekeratocyte
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC6525
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-0.176
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-0.0774
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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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: CNhs11337

Jaspar motifP-value
MA0002.20.0813
MA0003.10.232
MA0004.10.00579
MA0006.10.535
MA0007.10.0566
MA0009.10.316
MA0014.10.968
MA0017.10.0799
MA0018.20.195
MA0019.10.614
MA0024.10.00152
MA0025.10.751
MA0027.10.466
MA0028.10.894
MA0029.10.485
MA0030.10.608
MA0031.10.0872
MA0035.20.0221
MA0038.10.276
MA0039.20.976
MA0040.10.675
MA0041.10.32
MA0042.10.863
MA0043.10.877
MA0046.10.159
MA0047.20.951
MA0048.10.175
MA0050.10.348
MA0051.10.24
MA0052.10.85
MA0055.10.012
MA0057.10.531
MA0058.10.00304
MA0059.10.134
MA0060.10.193
MA0061.10.643
MA0062.20.121
MA0065.20.013
MA0066.10.36
MA0067.10.247
MA0068.10.817
MA0069.10.846
MA0070.10.00491
MA0071.10.108
MA0072.10.547
MA0073.10.858
MA0074.10.198
MA0076.10.798
MA0077.10.23
MA0078.10.501
MA0079.20.645
MA0080.26.28967e-6
MA0081.10.197
MA0083.10.624
MA0084.10.5
MA0087.10.982
MA0088.10.204
MA0090.10.0721
MA0091.10.0308
MA0092.10.646
MA0093.10.00847
MA0099.26.0691e-6
MA0100.10.961
MA0101.10.856
MA0102.20.139
MA0103.10.567
MA0104.20.297
MA0105.10.298
MA0106.10.00568
MA0107.10.987
MA0108.20.848
MA0111.10.485
MA0112.20.0442
MA0113.10.00235
MA0114.10.082
MA0115.10.571
MA0116.10.547
MA0117.10.376
MA0119.10.123
MA0122.10.137
MA0124.10.135
MA0125.10.849
MA0131.10.313
MA0135.10.164
MA0136.13.05681e-4
MA0137.20.142
MA0138.20.904
MA0139.10.591
MA0140.10.0147
MA0141.10.0428
MA0142.10.779
MA0143.10.696
MA0144.10.535
MA0145.10.48
MA0146.10.043
MA0147.10.37
MA0148.10.534
MA0149.10.428
MA0150.10.441
MA0152.10.563
MA0153.10.207
MA0154.10.244
MA0155.10.0343
MA0156.10.0369
MA0157.10.284
MA0159.10.157
MA0160.10.122
MA0162.10.0995
MA0163.10.115
MA0164.10.424
MA0258.10.0644
MA0259.10.7



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: CNhs11337

Novel motifP-value
10.844
100.792
1000.61
1010.657
1020.42
1030.434
1040.0537
1050.0859
1060.0711
1070.0131
1080.841
1090.0106
110.0372
1100.101
1110.994
1120.63
1130.263
1140.73
1150.815
1160.0657
1170.31
1180.516
1190.928
120.731
1200.598
1210.778
1220.311
1230.189
1240.576
1250.479
1260.99
1270.901
1280.555
1290.749
130.302
1300.105
1310.72
1320.444
1330.0112
1340.216
1350.948
1360.807
1370.258
1380.74
1390.947
140.836
1400.337
1410.659
1420.237
1430.482
1440.962
1450.318
1460.0451
1470.576
1480.863
1490.924
150.49
1500.259
1510.661
1520.0583
1530.347
1540.166
1550.32
1560.358
1570.0486
1580.52
1590.579
160.186
1600.0436
1610.607
1620.0439
1630.809
1640.368
1650.236
1660.675
1670.897
1680.92
1690.1
170.161
186.73356e-4
190.118
20.55
200.536
210.335
220.135
230.257
240.249
250.317
260.184
270.612
280.507
290.886
30.393
300.172
310.252
320.175
330.0796
340.0873
350.344
360.894
370.0469
380.663
390.395
40.635
400.0333
410.483
420.565
430.0842
440.147
450.252
460.174
470.16
480.0694
490.0648
50.575
500.235
510.342
520.447
530.667
540.337
550.636
560.128
570.318
580.329
590.0437
60.837
600.137
610.226
620.671
630.159
640.0631
650.0326
660.248
670.889
680.207
690.0364
70.986
700.00569
710.474
720.472
730.0258
740.963
750.375
760.902
770.018
780.595
790.684
80.105
800.815
810.467
820.887
830.198
840.641
850.0732
860.986
870.233
880.0888
890.0828
90.262
900.196
910.935
920.634
930.752
940.121
950.161
960.644
970.258
980.698
990.0112



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: CNhs11337


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)
0000008 (migratory cranial neural crest cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000133 (neurectodermal cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000333 (migratory neural crest cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002321 (embryonic cell)
0002363 (keratocyte)
0002371 (somatic cell)

UBERON: Anatomy
0000019 (camera-type eye)
0000020 (sense organ)
0000033 (head)
0000047 (simple eye)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000964 (cornea)
0000970 (eye)
0001032 (sensory system)
0001048 (primordium)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0001777 (substantia propria of cornea)
0001801 (anterior segment of eyeball)
0002050 (embryonic structure)
0002104 (visual system)
0002342 (neural crest)
0002346 (neurectoderm)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003075 (neural plate)
0003102 (surface structure)
0003566 (head connective tissue)
0003891 (stroma)
0004121 (ectoderm-derived structure)
0004456 (entire sense organ system)
0005423 (developing anatomical structure)
0005427 (corneal primordium)
0006598 (presumptive structure)
0007284 (presumptive neural plate)

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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