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FF:11421-118F8: 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 17:08, 29 March 2012


Name:Keratinocyte - epidermal, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
dev stage46 years old adult
sexfemale
age46
cell typekeratinocyte
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2568
catalog numberCA102-R10a
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-penis0.195
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-lymphoma0.339
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: CNhs12031

Jaspar motifP-value
MA0002.20.244
MA0003.10.663
MA0004.10.634
MA0006.10.187
MA0007.10.639
MA0009.10.224
MA0014.10.385
MA0017.10.485
MA0018.22.76225e-4
MA0019.10.352
MA0024.10.206
MA0025.10.408
MA0027.10.524
MA0028.10.195
MA0029.10.843
MA0030.10.00841
MA0031.10.00747
MA0035.20.952
MA0038.10.355
MA0039.28.19011e-4
MA0040.10.00847
MA0041.10.964
MA0042.10.0736
MA0043.10.00172
MA0046.10.37
MA0047.20.233
MA0048.10.265
MA0050.12.64583e-4
MA0051.10.00619
MA0052.19.06142e-4
MA0055.10.00467
MA0057.10.0415
MA0058.10.406
MA0059.10.168
MA0060.10.288
MA0061.10.838
MA0062.20.761
MA0065.20.0207
MA0066.10.0311
MA0067.10.0706
MA0068.12.92177e-6
MA0069.10.497
MA0070.10.92
MA0071.10.888
MA0072.10.221
MA0073.10.941
MA0074.10.996
MA0076.10.937
MA0077.10.947
MA0078.10.847
MA0079.20.964
MA0080.21.86587e-7
MA0081.10.0879
MA0083.10.0061
MA0084.10.118
MA0087.10.0981
MA0088.10.253
MA0090.10.00151
MA0091.10.227
MA0092.10.78
MA0093.10.522
MA0099.20.00913
MA0100.10.615
MA0101.10.316
MA0102.20.00556
MA0103.13.07058e-7
MA0104.20.184
MA0105.10.405
MA0106.16.6113e-12
MA0107.10.213
MA0108.20.0183
MA0111.10.2
MA0112.20.157
MA0113.10.843
MA0114.10.202
MA0115.10.689
MA0116.10.0105
MA0117.10.741
MA0119.10.173
MA0122.10.26
MA0124.10.506
MA0125.10.21
MA0131.10.881
MA0135.10.573
MA0136.15.42921e-4
MA0137.20.00103
MA0138.20.161
MA0139.10.35
MA0140.10.607
MA0141.10.553
MA0142.10.0139
MA0143.10.518
MA0144.10.222
MA0145.10.249
MA0146.10.123
MA0147.10.0973
MA0148.10.992
MA0149.10.00781
MA0150.10.782
MA0152.10.713
MA0153.10.512
MA0154.10.384
MA0155.10.307
MA0156.10.0284
MA0157.10.0505
MA0159.10.951
MA0160.10.962
MA0162.10.135
MA0163.10.0892
MA0164.10.934
MA0258.10.694
MA0259.10.413



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: CNhs12031

Novel motifP-value
10.141
100.49
1000.284
1010.348
1020.154
1030.182
1040.858
1050.437
1060.306
1070.108
1080.393
1092.64713e-4
110.115
1100.0589
1110.11
1120.259
1130.165
1140.173
1150.624
1160.683
1170.0665
1180.398
1190.268
120.646
1200.0122
1210.857
1220.366
1230.611
1240.163
1250.196
1260.248
1270.176
1280.661
1290.117
130.00619
1300.985
1310.463
1320.112
1330.0191
1340.109
1350.437
1360.0652
1370.448
1380.297
1390.868
140.883
1400.45
1410.0091
1420.278
1430.911
1440.207
1450.235
1460.176
1470.302
1480.411
1490.302
150.847
1500.122
1510.365
1520.0446
1530.83
1540.777
1550.795
1560.524
1570.606
1580.128
1590.734
160.0236
1600.0805
1610.0887
1620.337
1630.855
1640.209
1650.581
1660.622
1670.725
1680.369
1690.034
170.118
180.186
190.788
20.171
200.596
210.378
220.611
230.719
240.0178
250.909
260.0647
270.594
280.341
290.205
30.204
300.295
310.901
320.271
330.275
340.608
350.466
360.685
370.308
380.178
390.235
40.587
400.00732
410.67
420.349
430.541
440.0105
450.529
460.5
470.112
480.0193
490.85
50.692
500.442
510.647
520.805
530.632
540.853
550.901
560.29
570.198
580.79
590.227
60.446
600.409
610.387
620.97
630.122
640.271
650.372
660.223
670.731
680.531
690.19
70.411
700.149
710.0561
720.956
730.0234
740.168
750.0368
760.964
770.0629
780.0159
790.876
80.128
800.0595
810.517
820.769
830.835
840.302
850.716
860.698
870.05
880.987
890.0268
90.61
900.316
910.967
920.996
930.547
940.434
958.82679e-4
960.761
970.37
980.39
990.00366



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: CNhs12031


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)
0000035 (single fate stem cell)
0000036 (epithelial fate stem cell)
0000066 (epithelial cell)
0000076 (squamous epithelial cell)
0000079 (stratified epithelial cell)
0000114 (surface ectodermal cell)
0000221 (ectodermal cell)
0000237 (keratinizing barrier epithelial cell)
0000240 (stratified squamous epithelial cell)
0000255 (eukaryotic cell)
0000311 (keratin accumulating cell)
0000312 (keratinocyte)
0000325 (stuff accumulating cell)
0000357 (stratified epithelial stem cell)
0000362 (epidermal cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002077 (ecto-epithelial cell)
0002159 (general ecto-epithelial cell)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001003 (skin epidermis)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002097 (skin of body)
0002199 (integument)
0002416 (integumental system)
0002532 (epiblast (generic))
0003102 (surface structure)
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)
0007376 (outer epithelium)
0007383 (enveloping layer of ectoderm)

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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