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FF:11800-124C9: 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, donor2
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 number29
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-0.114
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0788
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-Whole1.051
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: CNhs13207

Jaspar motifP-value
MA0002.24.88395e-7
MA0003.10.0551
MA0004.10.559
MA0006.10.88
MA0007.10.974
MA0009.10.137
MA0014.10.654
MA0017.10.00875
MA0018.20.1
MA0019.10.611
MA0024.10.0133
MA0025.10.158
MA0027.10.74
MA0028.10.269
MA0029.10.255
MA0030.10.284
MA0031.10.525
MA0035.20.885
MA0038.10.028
MA0039.20.554
MA0040.10.43
MA0041.10.452
MA0042.10.278
MA0043.10.0674
MA0046.10.0444
MA0047.20.132
MA0048.10.803
MA0050.14.06443e-13
MA0051.12.25679e-6
MA0052.10.741
MA0055.10.815
MA0057.10.929
MA0058.10.347
MA0059.10.549
MA0060.11.87242e-5
MA0061.10.00388
MA0062.22.34337e-5
MA0065.20.0103
MA0066.10.149
MA0067.10.00718
MA0068.10.456
MA0069.10.913
MA0070.10.00806
MA0071.10.044
MA0072.10.596
MA0073.10.407
MA0074.10.316
MA0076.10.222
MA0077.10.064
MA0078.10.836
MA0079.20.655
MA0080.27.75163e-17
MA0081.14.53589e-5
MA0083.10.409
MA0084.10.395
MA0087.10.308
MA0088.10.464
MA0090.10.0049
MA0091.10.325
MA0092.10.413
MA0093.10.632
MA0099.20.621
MA0100.10.936
MA0101.10.036
MA0102.25.46128e-4
MA0103.10.531
MA0104.20.569
MA0105.12.21655e-5
MA0106.10.591
MA0107.10.0143
MA0108.25.55231e-10
MA0111.10.256
MA0112.26.5678e-4
MA0113.10.775
MA0114.10.063
MA0115.10.305
MA0116.13.67642e-5
MA0117.10.498
MA0119.10.328
MA0122.10.691
MA0124.10.243
MA0125.10.235
MA0131.10.637
MA0135.10.935
MA0136.13.20329e-20
MA0137.20.49
MA0138.20.724
MA0139.10.594
MA0140.10.905
MA0141.10.0158
MA0142.10.384
MA0143.10.81
MA0144.10.899
MA0145.10.23
MA0146.10.0249
MA0147.10.625
MA0148.10.563
MA0149.10.116
MA0150.10.1
MA0152.10.0322
MA0153.10.00547
MA0154.10.00214
MA0155.10.876
MA0156.14.32693e-11
MA0157.10.279
MA0159.10.0741
MA0160.10.00986
MA0162.10.639
MA0163.11.08892e-12
MA0164.10.907
MA0258.10.0103
MA0259.10.981



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: CNhs13207

Novel motifP-value
10.101
100.0232
1000.919
1010.34
1020.414
1030.266
1040.648
1050.285
1060.00816
1070.629
1080.905
1090.025
110.147
1100.192
1110.0176
1120.164
1130.513
1140.00287
1150.436
1160.981
1170.019
1180.0982
1190.172
120.354
1200.53
1210.95
1220.863
1234.08119e-4
1240.474
1250.0486
1260.156
1270.294
1280.0639
1290.967
130.0979
1300.268
1310.973
1320.0541
1330.0537
1340.671
1350.191
1360.631
1373.73245e-4
1380.259
1390.0139
140.318
1400.271
1410.723
1420.921
1430.0992
1440.914
1450.33
1460.791
1470.347
1480.0298
1490.619
150.108
1500.48
1510.24
1520.222
1530.459
1540.793
1550.0397
1560.883
1570.95
1580.144
1590.376
160.394
1600.515
1610.416
1620.699
1630.246
1640.123
1650.0379
1660.295
1670.0742
1680.649
1690.0166
170.345
180.196
190.281
20.803
200.49
210.412
220.253
230.336
240.332
250.125
260.0621
270.459
280.535
290.0652
30.0601
300.368
310.602
320.823
330.235
340.576
350.159
360.0513
370.0488
380.515
390.645
40.904
400.194
410.0743
420.279
430.0723
440.448
450.866
460.105
470.314
480.338
490.0877
50.133
500.995
510.394
520.347
530.318
540.417
550.407
560.769
570.752
580.027
590.119
60.994
600.0344
610.172
620.00662
630.48
640.342
650.374
660.268
670.217
680.983
690.509
70.147
700.0165
710.0436
720.299
730.129
740.494
750.0336
760.293
770.585
780.226
790.254
80.241
800.373
810.176
820.122
830.936
840.786
850.0501
860.0973
870.176
880.47
890.821
90.307
900.0815
910.43
920.385
930.399
940.015
950.0516
960.311
970.929
980.146
990.0808



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: CNhs13207


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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