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FF:11788-124B6: 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 17:30, 29 March 2012


Name:CD14+CD16- Monocytes, donor1
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
age25
cell typemonocyte
cell lineNA
companyNA
collaborationMichael Rehli (University of Regensberg)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number5
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-Peripheral0.0462
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-0.13
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.102
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.374
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0.317
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: CNhs13224

Jaspar motifP-value
MA0002.25.77261e-11
MA0003.10.0839
MA0004.10.64
MA0006.10.917
MA0007.10.83
MA0009.10.267
MA0014.10.428
MA0017.10.0166
MA0018.20.0063
MA0019.10.352
MA0024.10.00219
MA0025.12.27203e-5
MA0027.10.811
MA0028.10.713
MA0029.10.123
MA0030.10.494
MA0031.10.922
MA0035.20.376
MA0038.10.0886
MA0039.20.353
MA0040.10.228
MA0041.10.687
MA0042.10.287
MA0043.17.75407e-10
MA0046.10.138
MA0047.20.342
MA0048.10.899
MA0050.11.74909e-9
MA0051.13.91358e-4
MA0052.10.186
MA0055.10.85
MA0057.10.601
MA0058.10.39
MA0059.10.529
MA0060.19.27611e-8
MA0061.16.00009e-5
MA0062.24.95424e-4
MA0065.20.0187
MA0066.10.0446
MA0067.12.26708e-5
MA0068.10.444
MA0069.10.635
MA0070.10.0188
MA0071.10.148
MA0072.10.984
MA0073.10.385
MA0074.10.348
MA0076.10.933
MA0077.10.101
MA0078.10.67
MA0079.20.718
MA0080.24.79165e-16
MA0081.11.07846e-4
MA0083.10.453
MA0084.10.444
MA0087.10.327
MA0088.10.718
MA0090.10.0439
MA0091.10.709
MA0092.10.654
MA0093.10.686
MA0099.21.77072e-11
MA0100.10.88
MA0101.10.00118
MA0102.28.47201e-15
MA0103.10.24
MA0104.20.504
MA0105.13.15515e-7
MA0106.10.414
MA0107.13.5333e-4
MA0108.22.19885e-6
MA0111.10.495
MA0112.22.52136e-4
MA0113.10.93
MA0114.10.161
MA0115.10.893
MA0116.11.43203e-4
MA0117.10.054
MA0119.10.425
MA0122.10.845
MA0124.10.373
MA0125.10.206
MA0131.10.933
MA0135.10.273
MA0136.19.59547e-19
MA0137.20.431
MA0138.20.859
MA0139.10.85
MA0140.10.319
MA0141.10.0386
MA0142.10.395
MA0143.10.762
MA0144.10.245
MA0145.10.233
MA0146.10.0359
MA0147.10.629
MA0148.10.955
MA0149.10.08
MA0150.11.926e-8
MA0152.10.13
MA0153.10.0215
MA0154.10.00184
MA0155.10.805
MA0156.11.20202e-12
MA0157.10.469
MA0159.10.0342
MA0160.10.00982
MA0162.10.593
MA0163.18.52518e-8
MA0164.10.731
MA0258.10.00669
MA0259.10.848



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: CNhs13224

Novel motifP-value
10.132
100.0179
1000.943
1010.516
1020.614
1030.284
1040.674
1050.157
1060.00744
1070.616
1080.737
1090.0695
110.153
1100.305
1110.0382
1120.3
1130.654
1140.0138
1150.14
1160.856
1170.028
1180.0917
1190.411
120.347
1200.737
1210.975
1220.694
1230.0388
1240.875
1250.215
1260.176
1270.256
1280.0578
1290.99
130.108
1300.238
1310.631
1320.0263
1330.676
1340.568
1350.137
1360.801
1371.19291e-4
1380.121
1390.0296
140.346
1400.156
1410.322
1420.782
1430.0398
1440.724
1450.798
1460.691
1470.347
1480.0227
1490.596
150.123
1500.699
1510.284
1520.209
1530.772
1540.721
1550.258
1560.861
1570.574
1580.0422
1590.888
160.426
1600.519
1610.531
1620.258
1630.99
1640.0859
1650.108
1660.623
1670.2
1680.533
1690.00821
170.292
180.141
190.25
20.984
200.534
210.639
220.201
230.147
240.204
250.186
260.025
270.577
280.572
290.0662
30.114
300.497
310.711
320.663
330.178
340.494
350.19
360.0593
370.0643
380.465
390.883
40.9
400.078
410.019
420.38
430.0903
440.988
450.88
460.217
470.516
480.409
490.127
50.12
500.944
510.334
520.42
530.277
540.402
550.572
560.775
570.798
580.093
590.174
60.795
600.0607
610.232
620.04
630.577
640.334
650.248
660.127
670.638
680.821
690.821
70.164
700.0355
710.0196
720.23
730.104
740.0807
750.064
760.199
770.549
780.143
790.133
80.533
800.293
810.275
820.114
830.701
840.689
850.0255
860.0702
870.339
880.551
890.365
90.297
900.0561
910.364
920.329
930.331
940.0307
950.089
960.509
970.936
980.14
990.0158



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: CNhs13224


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)
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)

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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