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FF:11886-125D5: 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 17:34, 29 March 2012


Name:CD14+ monocytes - treated with Salmonella, donor3
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
sexfemale
age21
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD5-7
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-Peripheral0.82
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
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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
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-Whole0.21
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: CNhs13493

Jaspar motifP-value
MA0002.28.44604e-7
MA0003.10.611
MA0004.10.486
MA0006.10.992
MA0007.10.955
MA0009.10.381
MA0014.10.956
MA0017.10.131
MA0018.20.105
MA0019.10.478
MA0024.10.00289
MA0025.10.00234
MA0027.10.997
MA0028.10.116
MA0029.10.172
MA0030.10.138
MA0031.10.249
MA0035.20.322
MA0038.10.405
MA0039.20.606
MA0040.10.799
MA0041.10.563
MA0042.10.932
MA0043.12.48974e-8
MA0046.10.00919
MA0047.20.228
MA0048.10.541
MA0050.14.35008e-14
MA0051.16.47947e-9
MA0052.10.137
MA0055.10.417
MA0057.10.465
MA0058.10.292
MA0059.10.242
MA0060.14.45138e-9
MA0061.11.14583e-17
MA0062.20.815
MA0065.20.0295
MA0066.10.049
MA0067.14.3662e-5
MA0068.10.437
MA0069.10.993
MA0070.10.0338
MA0071.10.459
MA0072.10.814
MA0073.10.459
MA0074.10.0964
MA0076.10.12
MA0077.10.304
MA0078.10.594
MA0079.20.197
MA0080.21.12268e-11
MA0081.16.45881e-4
MA0083.10.427
MA0084.10.669
MA0087.10.925
MA0088.10.557
MA0090.10.344
MA0091.10.744
MA0092.10.378
MA0093.10.509
MA0099.22.69495e-43
MA0100.10.607
MA0101.11.36366e-21
MA0102.21.13909e-9
MA0103.10.0955
MA0104.20.51
MA0105.16.33891e-21
MA0106.10.735
MA0107.12.4707e-28
MA0108.20.816
MA0111.10.454
MA0112.25.71614e-4
MA0113.10.988
MA0114.10.157
MA0115.10.783
MA0116.12.49064e-4
MA0117.10.0813
MA0119.10.155
MA0122.10.675
MA0124.10.537
MA0125.10.2
MA0131.10.366
MA0135.10.535
MA0136.13.3778e-12
MA0137.20.0317
MA0138.20.458
MA0139.10.859
MA0140.10.384
MA0141.10.139
MA0142.10.624
MA0143.10.908
MA0144.10.0279
MA0145.10.514
MA0146.10.382
MA0147.10.569
MA0148.10.521
MA0149.10.22
MA0150.12.39499e-20
MA0152.10.959
MA0153.19.62537e-4
MA0154.11.83485e-4
MA0155.10.834
MA0156.19.96651e-8
MA0157.10.915
MA0159.10.019
MA0160.10.0676
MA0162.10.934
MA0163.13.74687e-8
MA0164.10.54
MA0258.10.0199
MA0259.10.544



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: CNhs13493

Novel motifP-value
10.114
100.0259
1000.966
1010.88
1020.986
1030.271
1040.54
1050.16
1062.20885e-4
1070.157
1080.81
1090.305
110.155
1100.182
1110.0757
1120.447
1130.379
1140.0235
1150.146
1160.866
1170.0907
1180.205
1190.117
120.264
1200.837
1210.751
1220.671
1230.365
1240.874
1250.148
1260.233
1270.484
1280.033
1290.383
130.0846
1300.295
1310.717
1320.126
1330.993
1340.431
1350.79
1360.936
1370.0405
1380.407
1390.0824
140.535
1400.481
1410.267
1420.244
1430.0276
1440.427
1450.351
1460.77
1470.849
1480.00876
1490.973
150.149
1500.269
1510.513
1520.334
1530.67
1540.769
1550.873
1560.724
1570.416
1580.0385
1590.273
160.339
1600.434
1610.347
1620.23
1630.12
1640.125
1650.228
1660.992
1670.294
1680.105
1690.0155
170.183
180.0944
190.522
20.564
200.169
210.68
220.296
230.0288
240.404
250.535
260.0529
270.561
280.324
290.307
30.117
300.393
310.756
320.483
330.193
340.67
350.104
360.0699
370.0712
380.37
390.777
40.975
400.226
410.0198
420.315
430.0218
440.614
450.679
460.199
470.57
480.489
490.123
50.317
500.992
510.572
520.29
530.526
540.469
550.716
560.708
570.806
580.18
590.171
60.764
600.0307
610.697
620.088
630.489
640.561
650.201
660.334
670.41
680.592
690.224
70.239
700.048
710.031
720.272
730.223
740.0689
750.166
760.173
770.427
780.116
790.961
80.375
800.189
810.357
820.232
830.0426
840.0416
850.0208
860.0578
870.542
880.762
890.218
90.311
900.0852
910.352
920.247
930.496
940.0972
950.61
960.353
970.535
980.141
990.116



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: CNhs13493


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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