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FF:11911-125G3: 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 17:37, 29 March 2012


Name:CD14-CD16+ Monocytes, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexmale
age23
cell typemonocyte
cell lineNA
companyNA
collaborationMichael Rehli (University of Regensberg)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number43-44
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-penis-0.102
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0729
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.296
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole1.006
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
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: CNhs13548

Jaspar motifP-value
MA0002.24.23902e-7
MA0003.10.0567
MA0004.10.497
MA0006.10.998
MA0007.10.98
MA0009.10.356
MA0014.10.426
MA0017.10.00446
MA0018.20.0493
MA0019.10.658
MA0024.10.0154
MA0025.10.0381
MA0027.10.727
MA0028.10.174
MA0029.10.296
MA0030.10.243
MA0031.10.375
MA0035.20.878
MA0038.10.209
MA0039.20.396
MA0040.10.365
MA0041.10.418
MA0042.10.307
MA0043.10.00523
MA0046.10.0521
MA0047.20.07
MA0048.10.841
MA0050.11.11814e-14
MA0051.11.75684e-6
MA0052.10.631
MA0055.10.932
MA0057.10.868
MA0058.10.333
MA0059.10.562
MA0060.13.45415e-4
MA0061.10.00371
MA0062.23.47867e-6
MA0065.20.0132
MA0066.10.225
MA0067.10.00276
MA0068.10.397
MA0069.10.884
MA0070.10.00509
MA0071.10.0848
MA0072.10.59
MA0073.10.54
MA0074.10.516
MA0076.10.104
MA0077.10.113
MA0078.10.88
MA0079.20.566
MA0080.23.82099e-16
MA0081.14.35811e-5
MA0083.10.452
MA0084.10.578
MA0087.10.363
MA0088.10.504
MA0090.10.0123
MA0091.10.437
MA0092.10.485
MA0093.10.566
MA0099.20.149
MA0100.10.973
MA0101.10.026
MA0102.22.13299e-4
MA0103.10.36
MA0104.20.414
MA0105.11.03579e-5
MA0106.10.61
MA0107.10.0119
MA0108.29.93058e-9
MA0111.10.289
MA0112.26.71577e-4
MA0113.10.909
MA0114.10.0514
MA0115.10.303
MA0116.12.17121e-5
MA0117.10.43
MA0119.10.292
MA0122.10.71
MA0124.10.229
MA0125.10.358
MA0131.10.529
MA0135.10.904
MA0136.18.3775e-20
MA0137.20.55
MA0138.20.56
MA0139.10.825
MA0140.10.872
MA0141.10.0196
MA0142.10.499
MA0143.10.82
MA0144.10.798
MA0145.10.232
MA0146.10.0382
MA0147.10.45
MA0148.10.525
MA0149.10.0603
MA0150.10.0427
MA0152.10.0628
MA0153.10.0127
MA0154.10.00203
MA0155.10.959
MA0156.13.66697e-12
MA0157.10.173
MA0159.10.0637
MA0160.10.00984
MA0162.10.698
MA0163.12.11583e-12
MA0164.10.93
MA0258.10.0103
MA0259.10.81



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: CNhs13548

Novel motifP-value
10.0869
100.0254
1000.787
1010.323
1020.452
1030.312
1040.567
1050.351
1060.0194
1070.815
1080.861
1090.0306
110.157
1100.231
1110.0324
1120.233
1130.387
1140.00666
1150.336
1160.946
1170.0192
1180.123
1190.275
120.296
1200.859
1210.963
1220.56
1232.30124e-4
1240.349
1250.0575
1260.158
1270.351
1280.0977
1290.982
130.125
1300.275
1310.878
1320.0416
1330.164
1340.716
1350.12
1360.744
1371.07535e-4
1380.281
1390.0129
140.393
1400.212
1410.513
1420.934
1430.158
1440.979
1450.287
1460.994
1470.428
1480.0576
1490.73
150.135
1500.525
1510.259
1520.343
1530.609
1540.783
1550.0743
1560.861
1570.738
1580.151
1590.223
160.482
1600.5
1610.575
1620.647
1630.265
1640.113
1650.126
1660.477
1670.048
1680.554
1690.0142
170.367
180.215
190.289
20.955
200.454
210.419
220.301
230.327
240.301
250.1
260.0656
270.55
280.478
290.08
30.0837
300.347
310.604
320.618
330.176
340.593
350.159
360.027
370.0547
380.471
390.737
40.918
400.146
410.0697
420.275
430.0869
440.617
450.943
460.139
470.331
480.353
490.0867
50.108
500.952
510.406
520.335
530.262
540.432
550.305
560.792
570.761
580.0289
590.148
60.782
600.0453
610.233
620.00807
630.513
640.343
650.37
660.367
670.249
680.825
690.608
70.136
700.0207
710.0456
720.244
730.137
740.385
750.032
760.214
770.628
780.27
790.267
80.282
800.315
810.182
820.146
830.746
840.696
850.0549
860.087
870.201
880.515
890.751
90.338
900.0542
910.46
920.482
930.444
940.0209
950.0637
960.281
970.982
980.104
990.0737



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: CNhs13548


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)
0000037 (hematopoietic stem cell)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000860 (classical monocyte)
0000875 (non-classical monocyte)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002057 (CD14-positive, CD16-negative classical monocyte)
0002087 (nongranular leukocyte)
0002194 (monopoietic cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002393 (intermediate monocyte)
0002396 (CD14-low, CD16-positive monocyte)
0002397 (CD14-positive, CD16-positive monocyte)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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