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|rna_box=125
|rna_box=125

Revision as of 18:40, 21 September 2012


Name:migratory langerhans cells, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexNA
ageNA
cell typelangerhans cell
cell lineNA
companyNA
collaborationTeunis Geijtenbeek
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberLC-A
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-penis0.0256
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-0.26
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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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



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: CNhs13535

Jaspar motifP-value
MA0002.24.62557e-4
MA0003.10.78
MA0004.10.314
MA0006.10.853
MA0007.10.601
MA0009.10.0677
MA0014.10.478
MA0017.10.0106
MA0018.20.778
MA0019.10.941
MA0024.10.173
MA0025.10.0353
MA0027.10.532
MA0028.10.883
MA0029.10.47
MA0030.10.856
MA0031.10.535
MA0035.20.738
MA0038.10.365
MA0039.20.037
MA0040.10.205
MA0041.10.213
MA0042.10.364
MA0043.10.0765
MA0046.10.948
MA0047.20.588
MA0048.10.927
MA0050.10.0266
MA0051.10.283
MA0052.10.231
MA0055.10.667
MA0057.10.883
MA0058.10.34
MA0059.10.88
MA0060.10.871
MA0061.12.85641e-11
MA0062.20.135
MA0065.20.0223
MA0066.10.399
MA0067.10.0819
MA0068.10.00931
MA0069.10.822
MA0070.10.321
MA0071.10.162
MA0072.10.708
MA0073.10.941
MA0074.10.318
MA0076.10.673
MA0077.10.648
MA0078.11
MA0079.20.602
MA0080.23.38193e-5
MA0081.10.237
MA0083.10.215
MA0084.10.141
MA0087.10.286
MA0088.10.206
MA0090.10.00744
MA0091.10.854
MA0092.10.566
MA0093.10.234
MA0099.20.792
MA0100.10.626
MA0101.12.76346e-9
MA0102.20.475
MA0103.10.199
MA0104.20.92
MA0105.11.26245e-14
MA0106.10.574
MA0107.15.82163e-12
MA0108.25.93683e-5
MA0111.10.207
MA0112.20.00118
MA0113.10.444
MA0114.10.0188
MA0115.10.145
MA0116.15.69789e-4
MA0117.10.382
MA0119.10.377
MA0122.10.642
MA0124.10.439
MA0125.10.707
MA0131.10.773
MA0135.10.247
MA0136.19.72851e-4
MA0137.20.751
MA0138.20.411
MA0139.10.142
MA0140.10.402
MA0141.10.027
MA0142.10.491
MA0143.10.258
MA0144.10.622
MA0145.10.117
MA0146.10.258
MA0147.10.852
MA0148.10.406
MA0149.10.204
MA0150.10.0171
MA0152.10.183
MA0153.10.0582
MA0154.13.69408e-4
MA0155.10.318
MA0156.10.457
MA0157.10.32
MA0159.10.0233
MA0160.10.0176
MA0162.10.687
MA0163.11.47626e-5
MA0164.10.539
MA0258.10.0132
MA0259.10.515



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: CNhs13535

Novel motifP-value
10.0173
100.0265
1000.944
1010.239
1020.492
1030.0287
1040.7
1050.121
1060.102
1070.919
1080.643
1090.0665
110.173
1100.274
1110.0425
1120.0311
1130.859
1140.00846
1150.267
1160.54
1170.0158
1180.0695
1190.0161
120.631
1200.707
1210.884
1220.842
1230.666
1240.182
1250.901
1260.049
1270.087
1280.0625
1290.253
130.0264
1300.85
1310.472
1320.385
1330.963
1340.957
1350.375
1360.636
1370.1
1380.761
1390.237
140.595
1400.00661
1410.65
1420.196
1430.379
1440.627
1450.352
1460.997
1470.175
1480.0431
1490.702
150.085
1500.672
1510.659
1520.491
1530.867
1540.265
1550.0661
1560.703
1570.65
1580.126
1590.986
160.202
1600.471
1610.0913
1620.648
1630.814
1640.428
1650.0286
1660.708
1670.661
1680.261
1690.0801
170.566
180.455
190.609
20.958
200.248
210.219
220.762
230.393
240.738
250.271
260.352
270.729
280.487
290.0938
30.0545
300.57
310.69
320.475
330.312
340.93
350.369
360.0776
370.187
380.363
390.989
40.408
400.156
410.28
420.19
430.124
440.0116
450.974
460.0873
470.137
480.263
490.076
50.439
500.874
510.269
520.195
530.528
540.433
550.557
560.881
570.169
580.0418
590.283
60.741
600.112
610.566
620.0238
630.486
640.32
650.508
660.244
670.255
680.75
690.699
70.103
700.027
710.0514
720.226
730.924
740.721
750.083
760.499
770.914
780.0284
790.857
80.513
800.98
810.394
820.172
830.231
840.257
850.401
860.319
870.381
880.306
890.535
90.94
900.00705
910.436
920.431
930.793
940.0813
950.152
960.00189
970.728
980.163
990.656



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: CNhs13535


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000219 (motile cell)
0000738 (leukocyte)
0000990 (conventional dendritic cell)
0000255 (eukaryotic cell)
0000451 (dendritic cell)
0000453 (Langerhans cell)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0011136 (human migratory langerhans cells sample)

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
CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)

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