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FF:11390-118C4: 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 17:00, 29 March 2012


Name:Neutrophils, 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 stage29 years old adult
sexfemale
age29
cell typeneutrophil
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNeu736
catalog number3H100-94-25
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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
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C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
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
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: CNhs11905

Jaspar motifP-value
MA0002.22.44277e-13
MA0003.10.234
MA0004.10.49
MA0006.10.362
MA0007.10.473
MA0009.10.113
MA0014.10.639
MA0017.10.151
MA0018.21.98783e-4
MA0019.10.534
MA0024.10.00227
MA0025.11.47707e-4
MA0027.10.789
MA0028.10.664
MA0029.10.436
MA0030.14.95949e-5
MA0031.10.0013
MA0035.20.91
MA0038.10.0903
MA0039.20.726
MA0040.10.0105
MA0041.10.332
MA0042.10.0677
MA0043.15.61227e-14
MA0046.10.194
MA0047.20.0586
MA0048.10.658
MA0050.17.1593e-5
MA0051.10.037
MA0052.10.0777
MA0055.10.0577
MA0057.10.26
MA0058.10.493
MA0059.10.385
MA0060.14.94136e-6
MA0061.14.31212e-10
MA0062.29.07635e-4
MA0065.20.0955
MA0066.10.0843
MA0067.11.81026e-4
MA0068.10.968
MA0069.10.527
MA0070.10.0429
MA0071.10.318
MA0072.10.904
MA0073.10.192
MA0074.10.381
MA0076.10.938
MA0077.10.282
MA0078.10.522
MA0079.20.747
MA0080.25.16442e-16
MA0081.12.16744e-5
MA0083.10.219
MA0084.10.971
MA0087.10.626
MA0088.10.112
MA0090.10.106
MA0091.10.804
MA0092.10.599
MA0093.10.374
MA0099.24.69803e-9
MA0100.10.939
MA0101.11.73674e-10
MA0102.21.56598e-15
MA0103.10.988
MA0104.20.12
MA0105.11.29583e-9
MA0106.10.186
MA0107.15.74117e-13
MA0108.20.00151
MA0111.10.474
MA0112.20.0149
MA0113.10.725
MA0114.10.619
MA0115.10.631
MA0116.10.00323
MA0117.10.0664
MA0119.10.953
MA0122.10.414
MA0124.10.738
MA0125.10.203
MA0131.10.804
MA0135.10.15
MA0136.11.31327e-20
MA0137.20.0107
MA0138.20.412
MA0139.10.981
MA0140.10.697
MA0141.10.159
MA0142.10.805
MA0143.10.738
MA0144.10.0103
MA0145.10.212
MA0146.10.135
MA0147.10.0847
MA0148.10.317
MA0149.10.956
MA0150.12.57977e-12
MA0152.10.0613
MA0153.10.164
MA0154.10.00291
MA0155.10.596
MA0156.18.8347e-15
MA0157.10.0102
MA0159.10.0515
MA0160.10.055
MA0162.10.971
MA0163.10.0182
MA0164.10.753
MA0258.10.0517
MA0259.10.115



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: CNhs11905

Novel motifP-value
10.285
100.0797
1000.253
1010.667
1020.832
1030.175
1040.666
1050.34
1062.99429e-4
1070.509
1080.429
1090.253
110.245
1100.671
1110.383
1120.361
1130.47
1140.0292
1150.553
1160.606
1170.0183
1180.144
1190.532
120.436
1200.653
1210.604
1220.85
1230.519
1240.84
1250.225
1260.118
1270.433
1280.0148
1290.807
130.556
1300.634
1310.767
1320.0787
1330.785
1340.506
1350.211
1360.581
1373.74809e-4
1380.148
1390.164
140.259
1400.51
1410.338
1420.484
1430.0252
1440.889
1450.943
1460.407
1470.49
1480.0665
1490.619
150.0713
1500.644
1510.378
1520.162
1530.433
1540.858
1550.147
1560.454
1570.697
1580.00724
1590.453
160.508
1600.612
1610.956
1620.14
1630.562
1640.17
1650.181
1660.929
1670.796
1680.528
1690.0967
170.352
180.157
190.377
20.923
200.619
210.908
220.164
230.00572
240.355
250.251
260.162
270.623
280.265
290.438
30.301
300.767
310.758
320.537
330.302
340.588
350.137
360.34
370.224
380.482
390.779
40.607
400.626
410.00445
420.573
430.0599
440.943
450.435
460.398
470.658
480.755
490.155
50.129
500.983
510.358
520.221
530.429
540.286
550.706
560.66
570.48
580.138
590.0882
60.735
600.0181
610.323
620.0382
630.742
640.569
650.272
660.206
670.556
680.269
690.847
70.279
700.187
710.0557
720.463
730.297
740.0732
750.209
760.242
770.853
780.292
790.515
80.677
800.028
810.41
820.0367
830.306
840.775
850.0677
860.0283
870.424
880.594
890.106
90.161
900.122
910.408
920.226
930.445
940.0509
950.711
960.43
970.971
980.172
990.0124



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: CNhs11905


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)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000081 (blood cell)
0000094 (granulocyte)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000775 (neutrophil)
0000837 (hematopoietic multipotent progenitor cell)
0000988 (hematopoietic cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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