NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE54296 Query DataSets for GSE54296
Status Public on Jan 14, 2015
Title Transcription Factor Highly Occupied Target (HOT) Regions of 145 Cell Lines
Sample organism Homo sapiens
Experiment type Other
Third-party reanalysis
Summary Purpose: 253 GSM Samples from GSE32970 and GSE29692 was reanalyzed to find the highly occupied target (HOT) regions of 154 cell lines.
Methods: 1. We assigned the binding sites of 542 TFs in 154 cell lines as GSE53962 (Our last submission). 2.We performed a Gaussian kernel density estimation across the genome with a bandwidth of 300 bp, using the centers of each of the TF binding peaks as points. Then, we scanned this density for peaks, and denoted each peak a TF region(Candidate region to find HOT regions).To determine the complexity of the TF region, we summed the Gaussian kernalized distance from the peak to each TF that contributed at least 0.1 to its strength. The TF region around eat peak was derived by finding the maximum distance (in bp) from the peak to a contributing TF, and then adding 150 bp (one half of the bandwidth). Each TF region is centered on the peak, and have a TF complexity value. 3.To define HOT region according to the TF complexity, we required a complexity cutoff for each cell line.To geometrically define the cutoff we first scaled the TF complexity such that the x and y axis were from 0-1. We then found the x axis point for which a line with a slope of 1 was tangent to the curve. We define this point as the cutoff value,TF region whose complexity above this point to be HOT region, and TF region complexity below that point to be lowly occupied target (LOT) regions.
Result: Using the binding sites of 542 TFs in 145 cell lines, we assigned a TF complexity score to each TF region corresponding to the number of distinct TFs bound, resulting in HOT regions of 145 cell lines.
 
Overall design TF HOT Regions of 145 Cell Lines. 54 GSM Samples from GSE32970 and 199 GSM Samples from GSE29692 were combined to 154 cell types.
 
Contributor(s) Shu W, Chen H, Li H
Citation(s) 26113264, 27633377
Submission date Jan 22, 2014
Last update date Oct 02, 2019
Contact name Wenjie Shu
E-mail(s) shuwj@bmi.ac.cn
Organization name Beijing Institute of Radiation Medicine
Street address Taiping Road 27
City Beijing
ZIP/Postal code 100850
Country China
 
Relations
Reanalysis of GSM736491
Reanalysis of GSM736492
Reanalysis of GSM736493
Reanalysis of GSM736494
Reanalysis of GSM736495
Reanalysis of GSM736496
Reanalysis of GSM736497
Reanalysis of GSM736498
Reanalysis of GSM736499
Reanalysis of GSM736500
Reanalysis of GSM736501
Reanalysis of GSM736502
Reanalysis of GSM736503
Reanalysis of GSM736504
Reanalysis of GSM736505
Reanalysis of GSM736506
Reanalysis of GSM736507
Reanalysis of GSM736508
Reanalysis of GSM736509
Reanalysis of GSM736510
Reanalysis of GSM736511
Reanalysis of GSM736512
Reanalysis of GSM736514
Reanalysis of GSM736515
Reanalysis of GSM736516
Reanalysis of GSM736517
Reanalysis of GSM736518
Reanalysis of GSM736519
Reanalysis of GSM736520
Reanalysis of GSM736521
Reanalysis of GSM736522
Reanalysis of GSM736523
Reanalysis of GSM736524
Reanalysis of GSM736525
Reanalysis of GSM736526
Reanalysis of GSM736527
Reanalysis of GSM736528
Reanalysis of GSM736529
Reanalysis of GSM736530
Reanalysis of GSM736531
Reanalysis of GSM736532
Reanalysis of GSM736533
Reanalysis of GSM736534
Reanalysis of GSM736535
Reanalysis of GSM736536
Reanalysis of GSM736537
Reanalysis of GSM736538
Reanalysis of GSM736539
Reanalysis of GSM736540
Reanalysis of GSM736541
Reanalysis of GSM736542
Reanalysis of GSM736543
Reanalysis of GSM736544
Reanalysis of GSM736545
Reanalysis of GSM736546
Reanalysis of GSM736547
Reanalysis of GSM736548
Reanalysis of GSM736549
Reanalysis of GSM736550
Reanalysis of GSM736551
Reanalysis of GSM736552
Reanalysis of GSM736553
Reanalysis of GSM736554
Reanalysis of GSM736555
Reanalysis of GSM736556
Reanalysis of GSM736557
Reanalysis of GSM736558
Reanalysis of GSM736559
Reanalysis of GSM736560
Reanalysis of GSM736561
Reanalysis of GSM736562
Reanalysis of GSM736563
Reanalysis of GSM736564
Reanalysis of GSM736565
Reanalysis of GSM736566
Reanalysis of GSM736567
Reanalysis of GSM736568
Reanalysis of GSM736569
Reanalysis of GSM736570
Reanalysis of GSM736571
Reanalysis of GSM736572
Reanalysis of GSM736573
Reanalysis of GSM736574
Reanalysis of GSM736575
Reanalysis of GSM736576
Reanalysis of GSM736577
Reanalysis of GSM736578
Reanalysis of GSM736579
Reanalysis of GSM736580
Reanalysis of GSM736581
Reanalysis of GSM736582
Reanalysis of GSM736583
Reanalysis of GSM736584
Reanalysis of GSM736585
Reanalysis of GSM736586
Reanalysis of GSM736587
Reanalysis of GSM736588
Reanalysis of GSM736589
Reanalysis of GSM736590
Reanalysis of GSM736591
Reanalysis of GSM736592
Reanalysis of GSM736593
Reanalysis of GSM736594
Reanalysis of GSM736595
Reanalysis of GSM736596
Reanalysis of GSM736597
Reanalysis of GSM736598
Reanalysis of GSM736599
Reanalysis of GSM736600
Reanalysis of GSM736601
Reanalysis of GSM736602
Reanalysis of GSM736603
Reanalysis of GSM736604
Reanalysis of GSM736605
Reanalysis of GSM736606
Reanalysis of GSM736607
Reanalysis of GSM736608
Reanalysis of GSM736609
Reanalysis of GSM736610
Reanalysis of GSM736611
Reanalysis of GSM736612
Reanalysis of GSM736613
Reanalysis of GSM736614
Reanalysis of GSM736615
Reanalysis of GSM736616
Reanalysis of GSM736617
Reanalysis of GSM736618
Reanalysis of GSM736619
Reanalysis of GSM736620
Reanalysis of GSM736621
Reanalysis of GSM736622
Reanalysis of GSM736623
Reanalysis of GSM736624
Reanalysis of GSM736625
Reanalysis of GSM736626
Reanalysis of GSM736627
Reanalysis of GSM736628
Reanalysis of GSM736629
Reanalysis of GSM736630
Reanalysis of GSM736631
Reanalysis of GSM736632
Reanalysis of GSM736633
Reanalysis of GSM736634
Reanalysis of GSM736635
Reanalysis of GSM736636
Reanalysis of GSM736637
Reanalysis of GSM736638
Reanalysis of GSM736639
Reanalysis of GSM816626
Reanalysis of GSM816627
Reanalysis of GSM816628
Reanalysis of GSM816629
Reanalysis of GSM816630
Reanalysis of GSM816631
Reanalysis of GSM816632
Reanalysis of GSM816633
Reanalysis of GSM816634
Reanalysis of GSM816635
Reanalysis of GSM816636
Reanalysis of GSM816637
Reanalysis of GSM816638
Reanalysis of GSM816639
Reanalysis of GSM816641
Reanalysis of GSM816642
Reanalysis of GSM816643
Reanalysis of GSM816644
Reanalysis of GSM816646
Reanalysis of GSM816647
Reanalysis of GSM816648
Reanalysis of GSM816649
Reanalysis of GSM816650
Reanalysis of GSM816651
Reanalysis of GSM816652
Reanalysis of GSM816653
Reanalysis of GSM816654
Reanalysis of GSM816655
Reanalysis of GSM816656
Reanalysis of GSM816657
Reanalysis of GSM816658
Reanalysis of GSM816659
Reanalysis of GSM816660
Reanalysis of GSM816661
Reanalysis of GSM816662
Reanalysis of GSM816663
Reanalysis of GSM816664
Reanalysis of GSM816665
Reanalysis of GSM816666
Reanalysis of GSM816667
Reanalysis of GSM816668
Reanalysis of GSM816669
Reanalysis of GSM816670
Reanalysis of GSM816671
Reanalysis of GSM816672
Reanalysis of GSM816673
Reanalysis of GSM931361
Reanalysis of GSM931362
Reanalysis of GSM1008572
Reanalysis of GSM1008592
Reanalysis of GSM1008593
Reanalysis of GSM1008594
Reanalysis of GSM1008595
Reanalysis of GSM1008604
Reanalysis of GSM1008605
Reanalysis of GSM1008606
Reanalysis of GSM1024742
Reanalysis of GSM1024743
Reanalysis of GSM1024745
Reanalysis of GSM1024747
Reanalysis of GSM1024751
Reanalysis of GSM1024760
Reanalysis of GSM1024763
Reanalysis of GSM1024765
Reanalysis of GSM1024766
Reanalysis of GSM1024770
Reanalysis of GSM1024788
Reanalysis of GSM1024791
Reanalysis of GSM1024792
Reanalysis of GSM1024795
Reanalysis of GSM1024777
Reanalysis of GSM1024775
Reanalysis of GSM1024750
Reanalysis of GSM1024768
Reanalysis of GSM1024785
Reanalysis of GSM1024746
Reanalysis of GSM1024787
Reanalysis of GSM1024773
Reanalysis of GSM1024757
Reanalysis of GSM1024781
Reanalysis of GSM1024779
Reanalysis of GSM1024790
Reanalysis of GSM1024749
Reanalysis of GSM1024753
Reanalysis of GSM1024740
Reanalysis of GSM1024739
Reanalysis of GSM1024744
Reanalysis of GSM1024741
Reanalysis of GSM1024759
Reanalysis of GSM1024774
Reanalysis of GSM1024754
Reanalysis of GSM1024778
Reanalysis of GSM1024789
Reanalysis of GSM1024782
Reanalysis of GSM1024780
Reanalysis of GSM1024776
Reanalysis of GSM1024769
Reanalysis of GSM1024786
Reanalysis of GSM1024794
Reanalysis of GSM1024748
Reanalysis of GSM1024756
Reanalysis of GSM1024793
Reanalysis of GSM1024752
Reanalysis of GSM1024758
Reanalysis of GSM1024755
BioProject PRJNA236115

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE54296_peak_files.tar.gz 121.3 Mb (ftp)(http) TAR
GSE54296_readme.txt 11.1 Kb (ftp)(http) TXT
Raw data not provided for this record
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap