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FF:11607-120I5: 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 17:11, 29 March 2012


Name:Keratocytes, donor2
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-ethanol-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-0.0787
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-0.0996
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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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: CNhs12095

Jaspar motifP-value
MA0002.20.0208
MA0003.10.173
MA0004.10.35
MA0006.10.641
MA0007.10.0193
MA0009.10.946
MA0014.10.894
MA0017.10.0636
MA0018.25.4157e-4
MA0019.10.931
MA0024.10.104
MA0025.10.337
MA0027.10.49
MA0028.10.11
MA0029.10.316
MA0030.10.1
MA0031.10.00575
MA0035.20.109
MA0038.10.515
MA0039.20.178
MA0040.10.436
MA0041.10.17
MA0042.10.797
MA0043.10.00197
MA0046.10.171
MA0047.20.571
MA0048.10.444
MA0050.11.02621e-6
MA0051.15.00046e-4
MA0052.10.199
MA0055.10.103
MA0057.10.0785
MA0058.10.506
MA0059.10.0962
MA0060.10.0539
MA0061.10.524
MA0062.20.00341
MA0065.20.00616
MA0066.10.0602
MA0067.10.161
MA0068.10.0922
MA0069.10.448
MA0070.10.0277
MA0071.10.00366
MA0072.10.222
MA0073.10.893
MA0074.10.308
MA0076.10.0047
MA0077.10.4
MA0078.10.64
MA0079.20.767
MA0080.20.00372
MA0081.10.263
MA0083.10.787
MA0084.10.691
MA0087.10.813
MA0088.10.169
MA0090.10.486
MA0091.10.0154
MA0092.10.368
MA0093.10.474
MA0099.24.43268e-7
MA0100.10.554
MA0101.10.903
MA0102.20.00666
MA0103.10.695
MA0104.20.497
MA0105.10.38
MA0106.10.0255
MA0107.10.861
MA0108.20.0493
MA0111.10.592
MA0112.20.00844
MA0113.10.0388
MA0114.10.0373
MA0115.10.695
MA0116.10.114
MA0117.10.153
MA0119.10.067
MA0122.10.669
MA0124.10.29
MA0125.10.729
MA0131.10.377
MA0135.10.0375
MA0136.12.09558e-4
MA0137.20.0361
MA0138.20.0216
MA0139.10.606
MA0140.10.221
MA0141.10.00199
MA0142.10.784
MA0143.10.993
MA0144.10.927
MA0145.10.192
MA0146.10.0254
MA0147.10.269
MA0148.10.415
MA0149.10.127
MA0150.10.203
MA0152.10.848
MA0153.10.321
MA0154.10.124
MA0155.10.0983
MA0156.10.00442
MA0157.10.301
MA0159.10.408
MA0160.10.0292
MA0162.10.118
MA0163.10.0138
MA0164.10.784
MA0258.10.0347
MA0259.10.71



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: CNhs12095

Novel motifP-value
10.315
100.919
1000.4
1010.768
1020.856
1030.157
1040.187
1050.0639
1060.114
1070.0804
1080.389
1090.0282
110.0127
1100.0796
1110.555
1120.35
1130.297
1140.507
1150.805
1160.133
1170.416
1180.647
1190.355
120.43
1200.171
1210.594
1220.815
1230.812
1240.593
1250.706
1260.666
1270.218
1280.0495
1290.373
130.357
1300.319
1310.819
1320.126
1330.457
1340.27
1350.748
1360.999
1370.172
1380.699
1390.413
140.934
1400.267
1410.55
1420.0889
1430.0303
1440.571
1450.136
1460.156
1470.235
1480.128
1490.0477
150.371
1500.421
1510.396
1520.145
1530.914
1540.457
1550.5
1560.11
1570.0836
1580.343
1590.829
160.257
1600.0441
1610.159
1620.141
1630.666
1640.494
1650.327
1660.728
1670.303
1680.489
1690.039
170.148
180.0684
190.105
20.217
200.604
210.738
220.0791
230.116
240.381
250.749
260.0571
270.124
280.315
290.644
30.304
300.22
310.396
325.81595e-4
330.888
340.222
350.84
360.571
370.208
380.221
390.607
40.249
400.0472
410.713
420.563
430.135
440.713
450.351
460.0877
470.175
480.105
490.121
50.479
500.501
510.201
520.565
530.908
540.259
550.521
560.226
570.3
580.819
590.0397
60.948
600.265
610.485
620.745
630.13
640.0525
650.0176
660.308
670.841
680.0383
690.0382
70.546
700.0254
710.177
720.973
730.0563
740.689
750.674
760.7
770.0241
780.748
790.159
80.0185
800.827
810.302
820.376
830.695
840.467
850.0903
860.874
870.176
880.305
890.0322
90.161
900.807
910.26
920.303
930.135
940.12
950.0988
960.178
970.866
980.146
990.0103



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: CNhs12095


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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