Cited by 26

The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.

Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data

Gong, Wuming, Koyano-Nakagawa, Naoko, Li, Tongbin, Garry, Daniel J·2015·BMC Bioinformatics

Overview

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.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1186/s12859-015-0460-0

Cites

5 of 5 references verified0 citation errors · 0 not checkable

Statistics

Verification

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.

A few free checks a day · papers already verified open instantly · results are public

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 75

  1. Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, et al. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012;151:206–20. · DOI
  2. He A, Kong SW, Ma Q, Pu WT. Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc Natl Acad Sci USA. 2011;108:5632–7. · DOI
  3. Paige SL, Thomas S, Stoick-Cooper CL, Wang H, Maves L, Sandstrom R, et al. A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development. Cell. 2012;151:221–32. · DOI
  4. Schlesinger J, Schueler M, Grunert M, Fischer JJ, Zhang Q, Krueger T, et al. The cardiac transcription network modulated by Gata4, Mef2a, Nkx2.5, Srf, histone modifications, and microRNAs. PLoS Genet. 2011;7:e1001313. · DOI
  5. Gallardo TD, Hammer RE, Garry DJ. RNA amplification and transcriptional profiling for analysis of stem cell populations. Genesis. 2003;37:57–63. · DOI
  6. Masino AM, Gallardo TD, Wilcox CA, Olson EN, Williams RS, Garry DJ. Transcriptional regulation of cardiac progenitor cell populations. Circ Res. 2004;95:389–97. · DOI
  7. Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science. 2003;301:102–5. · DOI · Paper page
  8. Schäfer J, Strimmer K. An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics. 2005;21:754–64. · DOI
  9. Zoppoli P, Morganella S, Ceccarelli M. TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. BMC Bioinformatics. 2010;11:154. · DOI · Paper page
  10. Roy S, Lagree S, Hou Z, Thomson JA, Stewart R, Gasch AP. Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks. PLoS Comput Biol. 2013;9:e1003252. · DOI
  11. Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 2004;431:308–12. · DOI
  12. Song L, Kolar M, Xing EP. Time-varying dynamic Bayesian networks. Advance Neural Inform Process Syst. 2009;22:1732–40.
  13. Vallat L, Kemper CA, Jung N, Maumy-Bertrand M, Bertrand F, Meyer N, et al. Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia. Proc Natl Acad Sci USA. 2013;110:459–64. · DOI
  14. Lèbre S, Becq J, Devaux F, Stumpf MPH, Lelandais G. Statistical inference of the time-varying structure of gene-regulation networks. BMC Syst Biol. 2010;4:130. · DOI
  15. Feizi S, Marbach D, Médard M, Kellis M. Network deconvolution as a general method to distinguish direct dependencies in networks. Nat Biotechnol. 2013;31:726–33. · DOI
  16. Ahmed A, Xing EP. Recovering time-varying networks of dependencies in social and biological studies. Proc Natl Acad Sci USA. 2009;106:11878–83. · DOI
  17. Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, et al. Wisdom of crowds for robust gene network inference. Nat Methods. 2012;9:796–804. · DOI · Paper page
  18. Peter IS, Davidson EH. A gene regulatory network controlling the embryonic specification of endoderm. Nature. 2011;474:635–9. · DOI
  19. Nishiyama A, Xin L, Sharov AA, Thomas M, Mowrer G, Meyers E, et al. Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors. Cell Stem Cell. 2009;5:420–33. · DOI
  20. Beer MA, Tavazoie S. Predicting gene expression from sequence. Cell. 2004;117:185–98. · DOI
  21. Mordelet F, Vert J-P. SIRENE: supervised inference of regulatory networks. Bioinformatics. 2008;24:i76–82. · DOI
  22. Christley S, Nie Q, Xie X. Incorporating existing network information into gene network inference. PLoS One. 2009;4:e6799. · DOI
  23. Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014;42(Database issue):D142–7. · DOI
  24. Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, et al. DNA-binding specificities of human transcription factors. Cell. 2013;152:327–39. · DOI
  25. Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 2008;133:1106–17. · DOI
  26. Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell. 2008;133:1266–76. · DOI · Paper page
  27. Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, et al. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res. 2010;20:861–73. · DOI · Paper page
  28. Macisaac KD, Gordon DB, Nekludova L, Odom DT, Schreiber J, Gifford DK, et al. A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics. 2006;22:423–9. · DOI
  29. Consortium UP. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2014;42(Database issue):D191–8.
  30. Zhao Y, Stormo GD. Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat Biotechnol. 2011;29:480–3. · DOI
  31. Gershenzon NI, Stormo GD, Ioshikhes IP. Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. Nucleic Acids Res. 2005;33:2290–301. · DOI
  32. May D, Blow MJ, Kaplan T, McCulley DJ, Jensen BC, Akiyama JA, et al. Large-scale discovery of enhancers from human heart tissue. Nat Genet. 2012;44:89–93. · DOI
  33. Murtha M, Tokcaer-Keskin Z, Tang Z, Strino F, Chen X, Wang Y, et al. FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells. Nat Methods. 2014;11:559–65. · DOI
  34. Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, et al. Super-Enhancers in the Control of Cell Identity and Disease. Cell. 2013;155:934–47. · DOI · Paper page
  35. Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet. 2010;42:806–10. · DOI · Paper page
  36. Yang J-H, Li J-H, Jiang S, Zhou H, Qu L-H. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res. 2013;41(Database issue):D177–87. · DOI
  37. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009;457:854–8. · DOI · Paper page
  38. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA. 2010;107:21931–6. · DOI · Paper page
  39. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011;473:43–9. · DOI · Paper page
  40. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 2009;459:108–12. · DOI · Paper page
  41. Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature. 2011;470:279–83. · DOI · Paper page
  42. Zentner GE, Tesar PJ, Scacheri PC. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res. 2011;21:1273–83. · DOI · Paper page
  43. Narlikar L, Sakabe NJ, Blanski AA, Arimura FE, Westlund JM, Nobrega MA, et al. Genome-wide discovery of human heart enhancers. Genome Res. 2010;20:381–92. · DOI
  44. Lim J-H, Iggo RD, Barker D. Models incorporating chromatin modification data identify functionally important p53 binding sites. Nucleic Acids Res. 2013;41:5582–93. · DOI
  45. Ernst J, Plasterer HL, Simon I, Bar-Joseph Z. Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Res. 2010;20:526–36. · DOI
  46. Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 2011;21:447–55. · DOI · Paper page
  47. Nishiyama A, Sharov AA, Piao Y, Amano M, Amano T, Hoang HG, et al. Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells. Sci Rep. 2013;3:1390. · DOI
  48. Correa-Cerro LS, Piao Y, Sharov AA, Nishiyama A, Cadet JS, Yu H, et al. Generation of mouse ES cell lines engineered for the forced induction of transcription factors. Sci Rep. 2011;1:167. · DOI
  49. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38:576–89. · DOI · Paper page
  50. Lyons I, Parsons LM, Hartley L, Li R, Andrews JE, Robb L, et al. Myogenic and morphogenetic defects in the heart tubes of murine embryos lacking the homeo box gene Nkx2-5. Genes Dev. 1995;9:1654–66. · DOI
  51. Tanaka M, Wechsler SB, Lee IW, Yamasaki N, Lawitts JA, Izumo S. Complex modular cis-acting elements regulate expression of the cardiac specifying homeobox gene Csx/Nkx2.5. Development. 1999;126:1439–50. · DOI
  52. Lien CL, Wu C, Mercer B, Webb R, Richardson JA, Olson EN. Control of early cardiac-specific transcription of Nkx2-5 by a GATA-dependent enhancer. Development. 1999;126:75–84. · DOI
  53. Searcy RD, Vincent EB, Liberatore CM, Yutzey KE. A GATA-dependent nkx-2.5 regulatory element activates early cardiac gene expression in transgenic mice. Development. 1998;125:4461–70. · DOI
  54. Klaus A, Saga Y, Taketo MM, Tzahor E, Birchmeier W. Distinct roles of Wnt/beta-catenin and Bmp signaling during early cardiogenesis. Proc Natl Acad Sci USA. 2007;104:18531–6. · DOI
  55. Heallen T, Morikawa Y, Leach J, Tao G, Willerson JT, Johnson RL, et al. Hippo signaling impedes adult heart regeneration. Development. 2013;140:4683–90. · DOI · Paper page
  56. Richter A, Valdimarsdottir L, Hrafnkelsdottir HE, Runarsson JF, Omarsdottir AR, Ward-van Oostwaard D, et al. BMP4 promotes EMT and mesodermal commitment in human embryonic stem cells via SLUG and MSX2. Stem Cells. 2014;32:636–48. · DOI
  57. Shen MM. Nodal signaling: developmental roles and regulation. Development. 2007;134:1023–34. · DOI
  58. Gregoire S, Karra R, Passer D, Deutsch M-A, Krane M, Feistritzer R, et al. Essential and unexpected role of Yin Yang 1 to promote mesodermal cardiac differentiation. Circ Res. 2013;112:900–10. · DOI
  59. Nentwich O, Dingwell KS, Nordheim A, Smith JC. Downstream of FGF during mesoderm formation in Xenopus: the roles of Elk-1 and Egr-1. Dev Biol. 2009;336:313–26. · DOI
  60. Khachigian LM. Early growth response-1 in cardiovascular pathobiology. Circ Res. 2006;98:186–91. · DOI
  61. Lei I, Gao X, Sham MH, Wang Z. SWI/SNF protein component BAF250a regulates cardiac progenitor cell differentiation by modulating chromatin accessibility during second heart field development. J Biol Chem. 2012;287:24255–62. · DOI
  62. Lickert H, Takeuchi JK, Von Both I, Walls JR, McAuliffe F, Adamson SL, et al. Baf60c is essential for function of BAF chromatin remodelling complexes in heart development. Nature. 2004;432:107–12. · DOI
  63. Yan Z, Wang Z, Sharova L, Sharov AA, Ling C, Piao Y, et al. BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse embryonic stem cells. Stem Cells. 2008;26:1155–65. · DOI
  64. Yu P, Xiao S, Xin X, Song C-X, Huang W, McDee D, et al. Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation. Genome Res. 2013;23:352–64. · DOI
  65. Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, et al. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell. 2013;152:570–83. · DOI
  66. Carè A, Catalucci D, Felicetti F, Bonci D, Addario A, Gallo P, et al. MicroRNA-133 controls cardiac hypertrophy. Nat Med. 2007;13:613–8. · DOI
  67. Le TD, Liu L, Liu B, Tsykin A, Goodall GJ, Satou K, et al. Inferring microRNA and transcription factor regulatory networks in heterogeneous data. BMC Bioinformatics. 2013;14:92. · DOI
  68. Geisler S, Coller J. RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol. 2013;14:699–712. · DOI
  69. Heng J-CD, Feng B, Han J, Jiang J, Kraus P, Ng J-H, et al. The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent cells. Cell Stem Cell. 2010;6:167–74. · DOI
  70. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105–11. · DOI
  71. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–95. · DOI · Paper page
  72. Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods. 2012;9:473–6. · DOI
  73. Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Statistic Software. 2010;33:1–22.
  74. Hong F, Breitling R, McEntee CW, Wittner BS, Nemhauser JL, Chory J. RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics. 2006;22:2825–7. · DOI
  75. Davison AC. Bootstrap methods and their application. 1997. · DOI · Paper page

Cited by

Sorted by citations

Metadata

Authors
Gong, W., Koyano-Nakagawa, N., Li, T., & Garry, D. J.
Venue
BMC Bioinformatics
Published
2015-03-07
Volume
16
Issue
1
ISSN
1471-2105
Cited by
26
References
5
Language
en

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