FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
Open accessAbstract
Summary: Next-generation sequencing can provide insight into protein–DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments. We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. The FindPeaks application can generate UCSC compatible custom ‘WIG’ track files from aligned-read files for short-read sequencing technology. The software application can be executed on any platform capable of running a Java Runtime Environment. Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads. Availability: The FindPeaks 3.1 package and manual, containing algorithm descriptions, usage instructions and examples, are available at http://www.bcgsc.ca/platform/bioinfo/software/findpeaks Source files for FindPeaks 3.1 are available for academic use. Contact: afejes@bcgsc.ca
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
ChIP-seq data sets were limited by applying thresholds defined by an FDR cutoff of 0.01 and by trimming at 20% of maximal height to remove flanks and separate composite regions.
“The data sets were limited by applying thresholds as defined by an FDR cutoff of 0.01 and by trimming at 20% of maximal height to remove flanks and separate composite regions (Fejes et al., 2008).”
From Hippo Signaling Influences HNF4A and FOXA2 Enhancer Switching during Hepatocyte Differentiation (2014) · cites this paper as Fejes et al., 2008
The Summary (p. 1729–1730) describes FindPeaks as a tool for identifying enriched regions in ChIP-seq data, but does not specify the cited thresholds. Searches for an FDR cutoff of 0.01 and trimming at 20% of maximal height found no passage in our copy addressing those settings or their stated purpose. (LLM, conf=0.74)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845 · see citing works
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927 · see citing works
Automated generation of heuristics for biological sequence comparison
Slater, G., & Birney, E. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-31 · Cited by 2,902 · see citing works
Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., et al. (2007) · Nature Methods · doi:10.1038/nmeth1068 · Cited by 1,454 · see citing works
Self-citationDynamic Regulation of Nucleosome Positioning in the Human Genome
Schones, D. E., Cui, K., Cuddapah, S., Roh, T., Barski, A., Wang, Z., Wei, G., & Zhao, K. (2008) · Cell · doi:10.1016/j.cell.2008.02.022 · Cited by 1,396 · see citing works
Morin, R. D., O’Connor, M. D., Griffith, M., Kuchenbauer, F., Delaney, A., Prabhu, A.-L., Zhao, Y., McDonald, H., Zeng, T., Hirst, M., et al. (2008) · Genome Research · doi:10.1101/gr.7179508 · Cited by 972 · see citing works
Genomic mapping by fingerprinting random clones: A mathematical analysis
Lander, E. S., & Waterman, M. S. (1988) · Genomics · doi:10.1016/0888-7543(88)90007-9 · Cited by 942 · see citing works
Taylor, K. H., Kramer, R. S., Davis, J. W., Guo, J., Duff, D. J., Xu, D. H., Caldwell, C. W., & Shi, H. (2007) · Cancer Research · doi:10.1158/0008-5472.can-07-1016 · Cited by 258 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · see citing works
Self-citationChIP–seq: advantages and challenges of a maturing technology
Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217 · see citing works
Identifying ChIP-seq enrichment using MACS
Feng, J., Liu, T., Qin, B., Zhang, Y., & Liu, X. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.101 · Cited by 1,805 · see citing works
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Zhu, L., Gazin, C., Lawson, N., Pagès, H., Lin, S. M., Lapointe, D. S., & Green, M. R. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-237 · Cited by 1,144 · see citing works
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
Zang, C., Schones, D. E., Zeng, C., Cui, K., Zhao, K., & Peng, W. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp340 · Cited by 1,043 · see citing works
Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways
Palmieri, M., Impey, S., Kang, H., di Ronza, A., Pelz, C., Sardiello, M., & Ballabio, A. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr306 · Cited by 1,022 · see citing works
Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells
Blaschke, K., Ebata, K. T., Karimi, M. M., Zepeda-Martínez, J. A., Goyal, P., Mahapatra, S., Tam, A., Laird, D. J., Hirst, M., Rao, A., et al. (2013) · Nature · doi:10.1038/nature12362 · Cited by 865 · see citing works
Next-Generation Sequencing: From Basic Research to Diagnostics
Voelkerding, K. V., Dames, S. A., & Durtschi, J. (2009) · Clinical Chemistry · doi:10.1373/clinchem.2008.112789 · Cited by 846 · see citing works
The Transcriptional and Epigenomic Foundations of Ground State Pluripotency
Marks, H., Kalkan, T., Menafra, R., Denissov, S., Jones, K. A., Hofemeister, H., Nichols, J., Kranz, A., Stewart, A., Smith, A. G., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.026 · Cited by 881 · see citing works
Vermeulen, M., Eberl, H. C., Matarese, F., Marks, H., Denissov, S., Butter, F., Lee, K. K., Olsen, J. V., Hyman, A. A., Stunnenberg, H. G., et al. (2010) · Cell · doi:10.1016/j.cell.2010.08.020 · Cited by 806 · see citing works
Malhotra, D., Portales-Casamar, É., Singh, A., Srivastava, S., Arenillas, D. J., Happel, C., Shyr, C., Wakabayashi, N., Kensler, T. W., Wasserman, W. W., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq212 · Cited by 796 · see citing works
Embryonic stem cell–specific microRNAs promote induced pluripotency
Judson, R. L., Babiarz, J., Venere, M., & Blelloch, R. H. (2009) · Nature Biotechnology · doi:10.1038/nbt.1535 · Cited by 677 · see citing works
Karimi, M. M., Goyal, P., Maksakova, I. A., Bilenky, M., Leung, D., Tang, J. X., Shinkai, Y., Mager, D. L., Jones, S., Hirst, M., et al. (2011) · Cell Stem Cell · doi:10.1016/j.stem.2011.04.004 · Cited by 535 · see citing works
Self-citationComputation for ChIP-seq and RNA-seq studies
Pepke, S., Wold, B. J., & Mortazavi, A. (2009) · Nature Methods · doi:10.1038/nmeth.1371 · Cited by 553 · see citing works
Insights from genomic profiling of transcription factors
Farnham, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2636 · Cited by 519 · see citing works
ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions
Schmidt, D., Wilson, M. D., Spyrou, C., Brown, G. D., Hadfield, J., & Odom, D. T. (2009) · Methods · doi:10.1016/j.ymeth.2009.03.001 · Cited by 515 · see citing works
Nielsen, R., Pedersen, T. Å., Hagenbeek, D., Moulos, P., Siersbæk, R., Megens, E., Denissov, S., Børgesen, M., Françoijs, K., Mandrup, S., et al. (2008) · Genes & Development · doi:10.1101/gad.501108 · Cited by 520 · see citing works
Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis
Gou, L., Dai, P., Yang, J.-H., Xue, Y., Hu, Y.-P., Zhou, Y., Kang, J.-Y., Wang, X., Li, H., Hua, M.-M., et al. (2014) · Cell Research · doi:10.1038/cr.2014.41 · Cited by 429 · see citing works
ChIP‐Seq of ERα and RNA polymerase II defines genes differentially responding to ligands
Welboren, W.-J., van Driel, M. A., Janssen‐Megens, E. M., van Heeringen, S. J., Sweep, F. C. G. J., Span, P. N., & Stunnenberg, H. G. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.88 · Cited by 395 · see citing works
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues
Ernst, J., & Kellis, M. (2015) · Nature Biotechnology · doi:10.1038/nbt.3157 · Cited by 352 · see citing works
MacLean, D., Jones, J. D. G., & Studholme, D. J. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2122 · Cited by 319 · see citing works
Application of 'next-generation' sequencing technologies to microbial genetics
MacLean, D., Jones, J. D. G., & Studholme, D. J. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2088 · Cited by 293 · see citing works
Tijssen, M. R., Cvejic, A., Joshi, A., Hannah, R., Ferreira, R., Forrai, A., Bellissimo, D. C., Oram, S. H., Smethurst, P. A., Wilson, N. K., et al. (2011) · Developmental Cell · doi:10.1016/j.devcel.2011.04.008 · Cited by 283 · see citing works
Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
Wilbanks, E. G., & Facciotti, M. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011471 · Cited by 284 · see citing works
Kwon, A. T.-J., Arenillas, D. J., Worsley-Hunt, R., & Wasserman, W. W. (2012) · G3 Genes Genomes Genetics · doi:10.1534/g3.112.003202 · Cited by 283 · see citing works
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
Sugimoto, Y., König, J., Hussain, S., Zupan, B., Curk, T., Frye, M., & Ule, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-8-r67 · Cited by 234 · see citing works
PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci
Salmon‐Divon, M., Dvinge, H., Koort, K., & Bertone, P. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-415 · Cited by 238 · see citing works
A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation
Seitan, V. C., Hao, B., Tachibana-Konwalski, K., Lavagnolli, T., Mira-Bontenbal, H., Brown, K. E., Teng, G., Carroll, T., Terry, A. V., Horan, K., et al. (2011) · Nature · doi:10.1038/nature10312 · Cited by 234 · see citing works
Boergesen, M., Pedersen, T. Å., Gross, B. S., van Heeringen, S. J., Hagenbeek, D., Bindesbøll, C., Caron, S., Lalloyer, F., Steffensen, K. R., Nebb, H. I., et al. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.06175-11 · Cited by 237 · see citing works
Distinct histone modifications in stem cell lines and tissue lineages from the early mouse embryo
Rugg‐Gunn, P. J., Cox, B., Ralston, A., & Rossant, J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914507107 · Cited by 235 · see citing works
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
Nix, D. A., Courdy, S., & Boucher, K. M. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-523 · Cited by 225 · see citing works
Guillon, N., Tirode, F., Boeva, V., Zynovyev, A., Barillot, E., & Delattre, O. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004932 · Cited by 218 · see citing works
Nuclear accumulation of HDAC4 in ATM deficiency promotes neurodegeneration in ataxia telangiectasia
Li, J., Chen, J., Ricupero, C. L., Hart, R. P., Schwartz, M. S., Kusnecov, A., & Herrup, K. (2012) · Nature Medicine · doi:10.1038/nm.2709 · Cited by 210 · see citing works
Markljung, E., Jiang, L., Jaffe, J. D., Mikkelsen, T. S., Wallerman, O., Larhammar, M., Zhang, X., Wang, L., Saenz-Vash, V., Gnirke, A., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000256 · Cited by 207 · see citing works
CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex
Saulière, J., Murigneux, V., Wang, Z., Marquenet, E., Barbosa, I., Tonquèze, O. L., Audic, Y., Paillard, L., Crollius, H. R., & Hir, H. L. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2420 · Cited by 199 · see citing works
Dellino, G. I., Cittaro, D., Piccioni, R., Luzi, L., Banfi, S., Segalla, S., Cesaroni, M., Mendoza-Maldonado, R., Giacca, M., & Pelicci, P. G. (2012) · Genome Research · doi:10.1101/gr.142331.112 · Cited by 200 · see citing works
Giresi, P. G., & Lieb, J. D. (2009) · Methods · doi:10.1016/j.ymeth.2009.03.003 · Cited by 198 · see citing works
Maksakova, I. A., Thompson, P. J., Goyal, P., Jones, S. J. M., Singh, P. B., Karimi, M. M., & Lorincz, M. C. (2013) · Epigenetics & Chromatin · doi:10.1186/1756-8935-6-15 · Cited by 185 · see citing works
Self-citationGenomic location analysis by ChIP‐Seq
Barski, A., & Zhao, K. (2009) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22077 · Cited by 169 · see citing works
Robertson, A. G., Bilenky, M., Tam, A., Zhao, Y., Zeng, T., Thiessen, N., Cezard, T., Fejes, A. P., Wederell, E. D., Cullum, R., et al. (2008) · Genome Research · doi:10.1101/gr.078519.108 · Cited by 182 · see citing works
Self-citationWeishi, Z., Prakash, C., Sum, C., Gong, Y., Li, Y., Kwok, J. J. T., Thiessen, N., Pettersson, S., Jones, S. J. M., Knapp, S., et al. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.413047 · Cited by 180 · see citing works
Self-citationKDM5B regulates embryonic stem cell self‐renewal and represses cryptic intragenic transcription
Xie, L., Pelz, C., Wang, W., Bashar, A., Varlamova, O., Shadle, S. C., & Impey, S. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.91 · Cited by 180 · see citing works
EZH2-mediated H3K27 trimethylation mediates neurodegeneration in ataxia-telangiectasia
Li, J., Hart, R. P., Mallimo, E. M., Swerdel, M. R., Kusnecov, A. W., & Herrup, K. (2013) · Nature Neuroscience · doi:10.1038/nn.3564 · Cited by 177 · see citing works
Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3′ UTRs
Zünd, D., Gruber, A. R., Zavolan, M., & Mühlemann, O. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2635 · Cited by 171 · see citing works
Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing
Horner, D. S., Pavesi, G., Castrignanò, T., Meo, P. D. D., Liuni, S., Sammeth, M., Picardi, E., & Pesole, G. (2009) · Briefings in Bioinformatics · doi:10.1093/bib/bbp046 · Cited by 173 · see citing works
Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin
Ing-Simmons, E., Seitan, V. C., Faure, A. J., Flicek, P., Carroll, T., Dekker, J., Fisher, A. G., Lenhard, B., & Merkenschlager, M. (2015) · Genome Research · doi:10.1101/gr.184986.114 · Cited by 167 · see citing works
Tee, W.-W., Shen, S. S., Oksuz, O., Narendra, V., & Reinberg, D. (2014) · Cell · doi:10.1016/j.cell.2014.01.009 · Cited by 165 · see citing works
Uniform, optimal signal processing of mapped deep-sequencing data
Kumar, V., Muratani, M., Rayan, N., Kraus, P., Lufkin, T., Ng, H., & Prabhakar, S. (2013) · Nature Biotechnology · doi:10.1038/nbt.2596 · Cited by 174 · see citing works
Neocentromeres Form Efficiently at Multiple Possible Loci in Candida albicans
Ketel, C. S., Wang, H. S. W., McClellan, M., Bouchonville, K. J., Selmecki, A. M., Lahav, T., Gerami‐Nejad, M., & Berman, J. G. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000400 · Cited by 164 · see citing works
Using ChIP-Seq Technology to Generate High-Resolution Profiles of Histone Modifications
O’Geen, H., Echipare, L., & Farnham, P. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-316-5_20 · Cited by 161 · see citing works
DiGuistini, S., Liao, N., Platt, D., Robertson, G., Seidel, M. A., Chan, S. K., Docking, R., Birol, İ., Holt, R. A., Hirst, M., et al. (2009) · Genome biology · doi:10.1186/gb-2009-10-9-r94 · Cited by 161 · see citing works
Self-citationPeakRanger: A cloud-enabled peak caller for ChIP-seq data
Feng, X., Grossman, R. L., & Stein, L. D. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-139 · Cited by 155 · see citing works
Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms
Rebollo, R., Karimi, M. M., Bilenky, M., Gagnier, L., Miceli-Royer, K., Zhang, Y., Goyal, P., Keane, T., Jones, S. J. M., Hirst, M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002301 · Cited by 157 · see citing works
Self-citationElo, L. L., Järvenpää, H., Tuomela, S., Raghav, S. K., Ahlfors, H., Laurila, K., Gupta, B., Lund, R., Tahvanainen, J., Hawkins, R. D., et al. (2010) · Immunity · doi:10.1016/j.immuni.2010.06.011 · Cited by 155 · see citing works
Deep and wide digging for binding motifs in ChIP-Seq data
Kulakovskiy, I. V., Boeva, V., Favorov, A. V., & Makeev, V. J. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq488 · Cited by 156 · see citing works
Boeva, V. (2016) · Frontiers in Genetics · doi:10.3389/fgene.2016.00024 · Cited by 152 · see citing works
AP4 is a mediator of epithelial–mesenchymal transition and metastasis in colorectal cancer
Jackstadt, R., Röh, S., Neumann, J. H. L., Jung, P., Hoffmann, R. F. G., Horst, D. A., Berens, C., Bornkamm, G. W., Kirchner, T., Menssen, A., et al. (2013) · The Journal of Experimental Medicine · doi:10.1084/jem.20120812 · Cited by 148 · see citing works
Harnessing genomics for evolutionary insights
Rokas, A., & Abbot, P. (2009) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.11.004 · Cited by 142 · see citing works
BayesPeak: Bayesian analysis of ChIP-seq data
Spyrou, C., Stark, R., Lynch, A. G., & Tavaré, S. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-299 · Cited by 132 · see citing works
Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells
Leddin, M., Perrod, C., Hoogenkamp, M., Ghani, S., Assi, S., Heinz, S., Wilson, N. K., Follows, G., Schönheit, J., Vockentanz, L., et al. (2011) · Blood · doi:10.1182/blood-2010-08-302976 · Cited by 131 · see citing works
Features that define the best ChIP-seq peak calling algorithms
Thomas, R., Thomas, S., Holloway, A. K., & Pollard, K. S. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw035 · Cited by 112 · see citing works
Waki, H., Nakamura, M., Yamauchi, T., Wakabayashi, K.-I., Yu, J., Hirose, L., Take, K., Sun, W., Iwabu, M., Okada‐Iwabu, M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002311 · Cited by 124 · see citing works
Wilson, N. K., Miranda‐Saavedra, D., Kinston, S., Bonadies, N., Foster, S. D., Calero‐Nieto, F. J., Dawson, M. A., Donaldson, I. J., Dumon, S., Frampton, J., et al. (2009) · Blood · doi:10.1182/blood-2009-01-200048 · Cited by 120 · see citing works
Zhang, Y., Lin, Y.-H., Johnson, T. D., Rozek, L. S., & Sartor, M. A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu372 · Cited by 120 · see citing works
Laajala, T. D., Raghav, S. K., Tuomela, S., Lahesmaa, R., Aittokallio, T. A., & Elo, L. L. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-618 · Cited by 119 · see citing works
Hippo Signaling Influences HNF4A and FOXA2 Enhancer Switching during Hepatocyte Differentiation
Alder, O., Cullum, R., Lee, S., Kan, A. C., Wei, W., Yi, Y., Garside, V. C., Bilenky, M., Griffith, M., Morrissy, A. S., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.08.046 · Cited by 113 · see citing works
“Clusters of overlapping extended reads were defined as enriched regions using FindPeaks2 (Fejes et al., 2008).”
MethodInfluentialSelf-citationDubois, F., Caby, S., Oger, F., Cosseau, C., Capron, M., Grunau, C., Dissous, C., & Pierce, R. J. (2009) · Molecular and Biochemical Parasitology · doi:10.1016/j.molbiopara.2009.06.001 · Cited by 113 · see citing works
Nallamilli, B. R. R., Zhang, J., Mujahid, H., Malone, B., Bridges, S. M., & Peng, Z. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003322 · Cited by 111 · see citing works
Extracting transcription factor targets from ChIP-Seq data
Tuteja, G., White, P., Schug, J., & Kaestner, K. H. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp536 · Cited by 108 · see citing works
On the detection and refinement of transcription factor binding sites using ChIP-Seq data
Hu, M., Yu, J., Taylor, J. M. G., Chinnaiyan, A. M., & Qin, Z. S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1180 · Cited by 103 · see citing works
Detection and Removal of Biases in the Analysis of Next-Generation Sequencing Reads
Schwartz, S., Ram, O., & Ast, G. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016685 · Cited by 101 · see citing works
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
Qin, Z. S., Yu, J., Shen, J., Maher, C. A., Hu, M., Sundaram, S. K., Yu, J., & Chinnaiyan, A. M. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-369 · Cited by 102 · see citing works
Paris, O., Ferraro, L., Grober, O. M. V., Ravo, M., Filippo, M. R. D., Giurato, G., Nassa, G., Tarallo, R., Cantarella, C., Rizzo, F. M., et al. (2012) · Oncogene · doi:10.1038/onc.2011.583 · Cited by 99 · see citing works
Integrative Analysis of ChIP-Chip and ChIP-Seq Dataset
Zhu, L. J. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-607-8_8 · Cited by 96 · see citing works
An integrated ChIP-seq analysis platform with customizable workflows
Γιαννοπούλου, Ε., & Elemento, O. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-277 · Cited by 92 · see citing works
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data
Althammer, S., González‐Vallinas, J., Ballaré, C., Beato, M., & Eyras, E. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr570 · Cited by 90 · see citing works
Chung, D., Kuan, P. F., Li, B., Sanalkumar, R., Liang, K., Bresnick, E. H., Dewey, C. N., & Keleş, S. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002111 · Cited by 89 · see citing works
Need, E. F., Selth, L. A., Harris, T. J., Birrell, S. N., Tilley, W. D., & Buchanan, G. (2012) · Molecular Endocrinology · doi:10.1210/me.2011-1314 · Cited by 87 · see citing works
High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology
Lan, X., Adams, C., Landers, M. A., Dudas, M., Krissinger, D., Marnellos, G., Bonneville, R., Xu, M., Wang, J., Huang, T. H. ‐., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022226 · Cited by 79 · see citing works
Using ChIP-seq Technology to Identify Targets of Zinc Finger Transcription Factors
O’Geen, H., Frietze, S. E., & Farnham, P. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-753-2_27 · Cited by 79 · see citing works
MACE: model based analysis of ChIP-exo
Wang, L.-G., Chen, J.-S., Wang, C., Uusküla-Reimand, L., Chen, K.-F., Medina-Rivera, A., Young, E. J., Zimmermann, M., Yan, H., Sun, Z.-F., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku846 · Cited by 72 · see citing works
Lesiak, A. J., Pelz, C., Ando, H., Zhu, M., Davare, M. A., Lambert, T. J., Hansen, K. F., Obrietan, K. H., Appleyard, S. M., Impey, S., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0064658 · Cited by 73 · see citing works
Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets
Worsley Hunt, R., & Wasserman, W. W. (2014) · Genome Biology · doi:10.1186/s13059-014-0412-4 · Cited by 73 · see citing works
Boeva, V., Surdez, D., Guillon, N., Tirode, F., Fejes, A. P., Delattre, O., & Barillot, E. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq217 · Cited by 72 · see citing works
Self-citationChromatin modification by SUMO-1 stimulates the promoters of translation machinery genes
Liu, H.-W., Zhang, J., Heine, G. F., Arora, M., Özer, H. G., Onti-Srinivasan, R., Huang, K., & Parvin, J. D. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks819 · Cited by 71 · see citing works
Epigenetic and transcriptional determinants of the human breast
Gascard, P. D., Bilenky, M., Sigaroudinia, M., Zhao, J., Li, L., Carles, A., Delaney, A. D., Tam, A., Kamoh, B., Cho, S. H., et al. (2015) · Nature Communications · doi:10.1038/ncomms7351 · Cited by 69 · see citing works
Self-citationVitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b
Ebata, K. T., Mesh, K., Liu, S., Bilenky, M., Fekete, A., Acker, M. G., Hirst, M., Garcia, B. A., & Ramalho‐Santos, M. (2017) · Epigenetics & Chromatin · doi:10.1186/s13072-017-0143-3 · Cited by 70 · see citing works
Self-citationPICS: Probabilistic Inference for ChIP-seq
Zhang, X., Robertson, G., Krzywinski, M. I., Ning, K., Droit, A., Jones, S. J. M., & Gottardo, R. (2010) · Biometrics · doi:10.1111/j.1541-0420.2010.01441.x · Cited by 70 · see citing works
Self-citationNext generation sequencing based approaches to epigenomics
Hirst, M., & Marra, M. A. (2010) · Briefings in Functional Genomics · doi:10.1093/bfgp/elq035 · Cited by 69 · see citing works
PPARalpha regulates the production of serum Vanin‐1 by liver
Rommelaere, S., Millet, V., Gensollen, T., Bourges, C., Eeckhoute, J., Hennuyer, N., Baugé, E., Chasson, L., Cacciatore, I., Staels, B., et al. (2013) · FEBS Letters · doi:10.1016/j.febslet.2013.09.046 · Cited by 69 · see citing works
Picking ChIP-seq peak detectors for analyzing chromatin modification experiments
Micsinai, M., Parisi, F., Strino, F., Asp, P., Dynlacht, B. D., & Kluger, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks048 · Cited by 66 · see citing works
Lun, D. S., Sherrid, A. M., Weiner, B., Sherman, D. R., & Galagan, J. E. (2009) · Genome biology · doi:10.1186/gb-2009-10-12-r142 · Cited by 66 · see citing works
Next‐generation technologies and data analytical approaches for epigenomics
Mensaert, K., Denil, S. L. I. J., Trooskens, G., Criekinge, W. V., Thas, O., & Meyer, T. D. (2013) · Environmental and Molecular Mutagenesis · doi:10.1002/em.21841 · Cited by 66 · see citing works
The p53/microRNA Network in Cancer: Experimental and Bioinformatics Approaches
Hünten, S., Siemens, H., Kaller, M., & Hermeking, H. (2012) · Advances in experimental medicine and biology · doi:10.1007/978-94-007-5590-1_5 · Cited by 65 · see citing works
Rye, M. B., Sætrom, P., & Drabløs, F. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1187 · Cited by 64 · see citing works
MER41 Repeat Sequences Contain Inducible STAT1 Binding Sites
Schmid, C. D., & Bücher, P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011425 · Cited by 64 · see citing works
Baker, K., Dhillon, T., Colas, I., Cook, N., Milne, I., Milne, L., Bayer, M., & Flavell, A. J. (2015) · The Plant Journal · doi:10.1111/tpj.12963 · Cited by 63 · see citing works
“Calling Cards” for DNA-Binding Proteins in Mammalian Cells
Wang, H., Mayhew, D. N., Chen, X., Johnston, M., & Mitra, R. D. (2012) · Genetics · doi:10.1534/genetics.111.137315 · Cited by 61 · see citing works
Three Distinct Patterns of Histone H3Y41 Phosphorylation Mark Active Genes
Dawson, M. A., Foster, S. D., Bannister, A. J., Robson, S. C., Hannah, R., Wang, X., Xhemalçe, B., Wood, A. D., Green, A. R., Göttgens, B., et al. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.016 · Cited by 60 · see citing works
Malone, B., Tan, F., Bridges, S. M., & Peng, Z. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025260 · Cited by 60 · see citing works
- Authors
- Fejes, A. P., Robertson, G., Bilenky, M., Varhol, R., Bainbridge, M., & Jones, S. J. M.
- Affiliations
- BC Cancer Agency (CA)
- Corresponding author
- Fejes, Anthony P.
- Jones, Steven J. M.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-07-03
- Volume
- 24
- Issue
- 15
- Pages
- 1729-1730
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC2638869
- OpenAlex
- W2141222038
- Cited by
- 272
- References
- 8
- Citations by year
- 2026: 1 · 2025: 2 · 2023: 6 · 2022: 2 · 2021: 4 · 2020: 2 · 2019: 4 · 2018: 1 · 2017: 9 · 2016: 12 · 2015: 16 · 2014: 23 · 2013: 34 · 2012: 36
- FWCI
- 16.47
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- eSpace (Curtin University) (submittedVersion)
- Funders
- Genome Canada
- Michael Smith Health Research BC
- Genome British Columbia
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- ChIP-seq, peak calling, gene enrichment, transcription factor binding sites, DNA fragment size distribution, short-read sequencing, protein-DNA interactions, UCSC Genome Browser
- MeSH terms
- Algorithms, Binding Sites, Chromosome Mapping, Pattern Recognition, Automated, Software, Transcription Factors, Sequence Analysis, DNA, Chromatin Immunoprecipitation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
