skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction

Abstract

Here, the molecular function of a gene is most commonly inferred by sequence similarity. Therefore, genes that lack sufficient sequence similarity to characterized genes (such as certain classes of transcriptional regulators) are difficult to classify using most function prediction algorithms and have remained uncharacterized. As a result, to identify novel transcriptional regulators systematically, we used a feature-based pipeline to screen protein families of unknown function. This method predicted 43 transcriptional regulator families in Arabidopsis thaliana, 7 families in Drosophila melanogaster, and 9 families in Homo sapiens. Literature curation validated 12 of the predicted families to be involved in transcriptional regulation. We tested 33 out of the 195 Arabidopsis putative transcriptional regulators for their ability to activate transcription of a reporter gene in planta and found twelve coactivators, five of which had no prior literature support. To investigate mechanisms of action in which the predicted regulators might work, we looked for interactors of an Arabidopsis candidate that did not show transactivation activity in planta and found that it might work with other members of its own family and a subunit of the Polycomb Repressive Complex 2 to regulate transcription. Our results demonstrate the feasibility of assigning molecular function to proteins ofmore » unknown function without depending on sequence similarity. In particular, we identified novel transcriptional regulators using biological features enriched in transcription factors. The predictions reported here should accelerate the characterization of novel regulators.« less

Authors:
 [1];  [1];  [2];  [1];  [2];  [3];  [2];  [1]
  1. Carnegie Institution for Science, Stanford, CA (United States)
  2. Univ. of Pennsylvania, Philadelphia, PA (United States)
  3. Carnegie Institution for Science, Stanford, CA (United States); Stanford Univ., Stanford, CA (United States)
Publication Date:
Research Org.:
Carnegie Institution for Science, Stanford, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1393512
Grant/Contract Number:  
SC0008769
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 18; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Genes with unknown function; Transcriptional regulators; Coactivators; Polycomb repressive complex 2

Citation Formats

Bossi, Flavia, Fan, Jue, Xiao, Jun, Chandra, Lilyana, Shen, Max, Dorone, Yanniv, Wagner, Doris, and Rhee, Seung Y. Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. United States: N. p., 2017. Web. doi:10.1186/s12864-017-3853-9.
Bossi, Flavia, Fan, Jue, Xiao, Jun, Chandra, Lilyana, Shen, Max, Dorone, Yanniv, Wagner, Doris, & Rhee, Seung Y. Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. United States. doi:10.1186/s12864-017-3853-9.
Bossi, Flavia, Fan, Jue, Xiao, Jun, Chandra, Lilyana, Shen, Max, Dorone, Yanniv, Wagner, Doris, and Rhee, Seung Y. Mon . "Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction". United States. doi:10.1186/s12864-017-3853-9. https://www.osti.gov/servlets/purl/1393512.
@article{osti_1393512,
title = {Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction},
author = {Bossi, Flavia and Fan, Jue and Xiao, Jun and Chandra, Lilyana and Shen, Max and Dorone, Yanniv and Wagner, Doris and Rhee, Seung Y.},
abstractNote = {Here, the molecular function of a gene is most commonly inferred by sequence similarity. Therefore, genes that lack sufficient sequence similarity to characterized genes (such as certain classes of transcriptional regulators) are difficult to classify using most function prediction algorithms and have remained uncharacterized. As a result, to identify novel transcriptional regulators systematically, we used a feature-based pipeline to screen protein families of unknown function. This method predicted 43 transcriptional regulator families in Arabidopsis thaliana, 7 families in Drosophila melanogaster, and 9 families in Homo sapiens. Literature curation validated 12 of the predicted families to be involved in transcriptional regulation. We tested 33 out of the 195 Arabidopsis putative transcriptional regulators for their ability to activate transcription of a reporter gene in planta and found twelve coactivators, five of which had no prior literature support. To investigate mechanisms of action in which the predicted regulators might work, we looked for interactors of an Arabidopsis candidate that did not show transactivation activity in planta and found that it might work with other members of its own family and a subunit of the Polycomb Repressive Complex 2 to regulate transcription. Our results demonstrate the feasibility of assigning molecular function to proteins of unknown function without depending on sequence similarity. In particular, we identified novel transcriptional regulators using biological features enriched in transcription factors. The predictions reported here should accelerate the characterization of novel regulators.},
doi = {10.1186/s12864-017-3853-9},
journal = {BMC Genomics},
number = 1,
volume = 18,
place = {United States},
year = {2017},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Figures / Tables:

Fig. 1 Fig. 1: Feature-based prediction pipeline to identify novel transcriptional regulator families. a Pipeline work flow: First, Arabidopsis protein families were filtered based on their size and the GO annotations of their members. Then, uncharacterized families with more than 2 members were filtered based on subcellular localization patterns using Yloc [98],more » percentage of disordered residues using Predisorder [99], and the ability of at least one member to activate transcription of a reporter gene in yeast (autoactivation) [22, 103–107]. Numbers in the Venn diagram represent the number of families with most members being nuclear localized (blue), high percentage of disordered residues (green) and autoactivation in yeast (red). Families that met all criteria (intersection of the Venn diagram) were considered as candidate regulator families. b-j Proportion of proteins predicted to contain nuclear localization signal (NLS) (b-d), distribution of the percentage of disordered amino acid residues (e-g), and proportion of proteins with autoactivation activity (h-j) in the background (white), TFs (dark gray), and predicted regulators (light gray). The background corresponds to all proteins in Arabidopsis (b,e,h), fruit fly (c, f, i), or human (d, g, j) genomes or the set of proteins that were tested for autoactivation in yeast (h, i, j). * = p-value <0.0001, chi-square test with Yates correction (b-d and h-j) or t-test (e-g)« less

Save / Share:

Works referenced in this record:

Specific DNA binding of GAL4, a positive regulatory protein of yeast
journal, April 1985


Targeting Polycomb systems to regulate gene expression: modifications to a complex story
journal, September 2015

  • Blackledge, Neil P.; Rose, Nathan R.; Klose, Robert J.
  • Nature Reviews Molecular Cell Biology, Vol. 16, Issue 11
  • DOI: 10.1038/nrm4067

New GATEWAY vectors for High Throughput Analyses of Protein–Protein Interactions by Bimolecular Fluorescence Complementation
journal, September 2009

  • Gehl, Christian; Waadt, Rainer; Kudla, Jörg
  • Molecular Plant, Vol. 2, Issue 5
  • DOI: 10.1093/mp/ssp040

Predicting protein function from sequence and structure
journal, December 2007

  • Lee, David; Redfern, Oliver; Orengo, Christine
  • Nature Reviews Molecular Cell Biology, Vol. 8, Issue 12
  • DOI: 10.1038/nrm2281

The glutamine-rich activation domains of human Sp1 do not stimulate transcription in Saccharomyces cerevisiae.
journal, February 1995

  • Ponticelli, A. S.; Pardee, T. S.; Struhl, K.
  • Molecular and Cellular Biology, Vol. 15, Issue 2
  • DOI: 10.1128/MCB.15.2.983

Ectopic expression of the Arabidopsis transcriptional activator Athb-1 alters leaf cell fate in tobacco.
journal, November 1995


A Protein Interaction Map of Drosophila melanogaster
journal, December 2003


I-TASSER: a unified platform for automated protein structure and function prediction
journal, March 2010

  • Roy, Ambrish; Kucukural, Alper; Zhang, Yang
  • Nature Protocols, Vol. 5, Issue 4
  • DOI: 10.1038/nprot.2010.5

Mutations in FAM134B, encoding a newly identified Golgi protein, cause severe sensory and autonomic neuropathy
journal, October 2009

  • Kurth, Ingo; Pamminger, Torsten; Hennings, J. Christopher
  • Nature Genetics, Vol. 41, Issue 11
  • DOI: 10.1038/ng.464

The BioGRID interaction database: 2015 update
journal, November 2014

  • Chatr-aryamontri, Andrew; Breitkreutz, Bobby-Joe; Oughtred, Rose
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1204

The MADF–BESS domain factor Dip3 potentiates synergistic activation by Dorsal and Twist
journal, October 2002


The Arabidopsis thaliana mitogen-activated protein kinases MPK3 and MPK6 target a subclass of ‘VQ-motif’-containing proteins to regulate immune responses
journal, April 2014

  • Pecher, Pascal; Eschen-Lippold, Lennart; Herklotz, Siska
  • New Phytologist, Vol. 203, Issue 2
  • DOI: 10.1111/nph.12817

Comparative analyses of nuclear proteome: extending its function
journal, January 2013

  • Narula, Kanika; Datta, Asis; Chakraborty, Niranjan
  • Frontiers in Plant Science, Vol. 4
  • DOI: 10.3389/fpls.2013.00100

An empirical framework for binary interactome mapping
journal, December 2008

  • Venkatesan, Kavitha; Rual, Jean-François; Vazquez, Alexei
  • Nature Methods, Vol. 6, Issue 1
  • DOI: 10.1038/nmeth.1280

Conservation of Glutamine-Rich Transactivation Function between Yeast and Humans
journal, April 2000


A novel mechanism of regulation of the anti-metastatic miR-31 by EMSY in breast cancer
journal, November 2014

  • Mulrane, Laoighse; Gallagher, William M.; O’Connor, Darran P.
  • Breast Cancer Research, Vol. 16, Issue 6
  • DOI: 10.1186/s13058-014-0467-x

Plant organ size control: AINTEGUMENTA regulates growth and cell numbers during organogenesis
journal, January 2000

  • Mizukami, Y.; Fischer, R. L.
  • Proceedings of the National Academy of Sciences, Vol. 97, Issue 2
  • DOI: 10.1073/pnas.97.2.942

Analysis of Polygenic Mutants Suggests a Role for Mediator in Regulating Transcriptional Activation Distance in Saccharomyces cerevisiae
journal, August 2015


PreDisorder: ab initio sequence-based prediction of protein disordered regions
journal, January 2009


Functionally Enigmatic Genes: A Case Study of the Brain Ignorome
journal, February 2014


Position-dependent transcriptional regulation of the murine dihydrofolate reductase promoter by the E2F transactivation domain.
journal, April 1997

  • Fry, C. J.; Slansky, J. E.; Farnham, P. J.
  • Molecular and Cellular Biology, Vol. 17, Issue 4
  • DOI: 10.1128/MCB.17.4.1966

The Roles of Auxin Response Factor Domains in Auxin-Responsive Transcription
journal, January 2003

  • Tiwari, Shiv B.; Hagen, Gretchen; Guilfoyle, Tom
  • The Plant Cell, Vol. 15, Issue 2
  • DOI: 10.1105/tpc.008417

Structure(?) and function of acidic transcription activators
journal, February 1993


Glutamine-rich Domains Activate Transcription in Yeast Saccharomyces cerevisiae
journal, September 1998


The pEAQ vector series: the easy and quick way to produce recombinant proteins in plants
journal, March 2013


Transcription factors: from enhancer binding to developmental control
journal, August 2012

  • Spitz, François; Furlong, Eileen E. M.
  • Nature Reviews Genetics, Vol. 13, Issue 9
  • DOI: 10.1038/nrg3207

Crossing the line between activation and repression
journal, January 2005


Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis
journal, June 2007


GeBP , the first member of a new gene family in Arabidopsis , encodes a nuclear protein with DNA-binding activity and is regulated by KNAT1
journal, January 2003


Quantitative Interaction Proteomics and Genome-wide Profiling of Epigenetic Histone Marks and Their Readers
journal, September 2010


In vivo analysis of plant promoters and transcription factors by agroinfiltration of tobacco leaves
journal, June 2000


Mammalian transcription factors in yeast: strangers in a familiar land
journal, January 2002

  • Kennedy, Brian K.
  • Nature Reviews Molecular Cell Biology, Vol. 3, Issue 1
  • DOI: 10.1038/nrm704

The COMBREX Project: Design, Methodology, and Initial Results
journal, August 2013


Arabidopsis Transcription Factors: Genome-Wide Comparative Analysis Among Eukaryotes
journal, December 2000


Cooperative DNA binding of the yeast transcriptional activator GAL4.
journal, January 1988

  • Giniger, E.; Ptashne, M.
  • Proceedings of the National Academy of Sciences, Vol. 85, Issue 2
  • DOI: 10.1073/pnas.85.2.382

Direct Repression of KNOX Loci by the ASYMMETRIC LEAVES1 Complex of Arabidopsis
journal, January 2008


Arabidopsis WUSCHEL Is a Bifunctional Transcription Factor That Acts as a Repressor in Stem Cell Regulation and as an Activator in Floral Patterning
journal, November 2009

  • Ikeda, Miho; Mitsuda, Nobutaka; Ohme-Takagi, Masaru
  • The Plant Cell, Vol. 21, Issue 11
  • DOI: 10.1105/tpc.109.069997

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations
journal, November 2014

  • dos Santos, G.; Schroeder, A. J.; Goodman, J. L.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1099

Inferring Function Using Patterns of Native Disorder in Proteins
journal, January 2007


Towards a proteome-scale map of the human protein–protein interaction network
journal, September 2005

  • Rual, Jean-François; Venkatesan, Kavitha; Hao, Tong
  • Nature, Vol. 437, Issue 7062
  • DOI: 10.1038/nature04209

Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis
journal, March 2008

  • Horan, Kevin; Jang, Charles; Bailey-Serres, Julia
  • Plant Physiology, Vol. 147, Issue 1
  • DOI: 10.1104/pp.108.117366

EMSY Links the BRCA2 Pathway to Sporadic Breast and Ovarian Cancer
journal, November 2003


GeBP and GeBP-Like Proteins Are Noncanonical Leucine-Zipper Transcription Factors That Regulate Cytokinin Response in Arabidopsis
journal, December 2007

  • Chevalier, Florian; Perazza, Daniel; Laporte, Frédéric
  • Plant Physiology, Vol. 146, Issue 3
  • DOI: 10.1104/pp.107.110270

The role of JAGGED in shaping lateral organs
journal, March 2004


An efficient algorithm for large-scale detection of protein families
journal, April 2002


Polycomb repression in the regulation of growth and development in Arabidopsis
journal, February 2015


The Breast Cancer Oncogene EMSY Represses Transcription of Antimetastatic microRNA miR-31
journal, March 2014


Diversity of Polycomb group complexes in plants: same rules, different players?
journal, September 2009


Ensembl Genomes 2016: more genomes, more complexity
journal, November 2015

  • Kersey, Paul Julian; Allen, James E.; Armean, Irina
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1209

Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription
journal, July 2016


Gateway Binary Vectors with the Bialaphos Resistance Gene, bar , as a Selection Marker for Plant Transformation
journal, June 2010

  • Nakamura, Shinya; Mano, Shoji; Tanaka, Yuji
  • Bioscience, Biotechnology, and Biochemistry, Vol. 74, Issue 6
  • DOI: 10.1271/bbb.100184

Transcriptional activators in yeast
journal, February 2006


dOct2, a Drosophila Oct transcription factor that functions in yeast.
journal, August 1992

  • Prakash, K.; Fang, X. D.; Engelberg, D.
  • Proceedings of the National Academy of Sciences, Vol. 89, Issue 15
  • DOI: 10.1073/pnas.89.15.7080

Late Cornified Envelope Family in Differentiating Epithelia—Response to Calcium and Ultraviolet Irradiation
journal, May 2005


Variant PRC1 Complex-Dependent H2A Ubiquitylation Drives PRC2 Recruitment and Polycomb Domain Formation
journal, June 2014


Interaction of Polycomb-group proteins controlling flowering in Arabidopsis
journal, November 2004


Arabidopsis Ethylene-Responsive Element Binding Factors Act as Transcriptional Activators or Repressors of GCC Box–Mediated Gene Expression
journal, March 2000

  • Fujimoto, Susan Y.; Ohta, Masaru; Usui, Akemi
  • The Plant Cell, Vol. 12, Issue 3
  • DOI: 10.1105/tpc.12.3.393

Activation domains of transcriptional regulatory proteins
journal, July 1993

  • Johnson, Peter F.; Sterneck, Esta; Williams, Simon C.
  • The Journal of Nutritional Biochemistry, Vol. 4, Issue 7
  • DOI: 10.1016/0955-2863(93)90069-9

The GOA database: Gene Ontology annotation updates for 2015
journal, November 2014

  • Huntley, Rachael P.; Sawford, Tony; Mutowo-Meullenet, Prudence
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1113

Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry
journal, November 2015

  • Huang, He; Alvarez, Sophie; Bindbeutel, Rebecca
  • Molecular & Cellular Proteomics, Vol. 15, Issue 1
  • DOI: 10.1074/mcp.M115.054064

Arabidopsis Polycomb Repressive Complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes
journal, January 2013


Integrating mRNA Processing with Transcription
journal, February 2002


Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

Human Transcription Factors Contain a High Fraction of Intrinsically Disordered Regions Essential for Transcriptional Regulation
journal, June 2006

  • Minezaki, Yoshiaki; Homma, Keiichi; Kinjo, Akira R.
  • Journal of Molecular Biology, Vol. 359, Issue 4
  • DOI: 10.1016/j.jmb.2006.04.016

LATERAL ORGAN BOUNDARIES defines a new family of DNA-binding transcription factors and can interact with specific bHLH proteins
journal, October 2007

  • Husbands, Aman; Bell, Elizabeth M.; Shuai, Bin
  • Nucleic Acids Research, Vol. 35, Issue 19
  • DOI: 10.1093/nar/gkm775

Phytozome: a comparative platform for green plant genomics
journal, November 2011

  • Goodstein, David M.; Shu, Shengqiang; Howson, Russell
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr944

Targeting Polycomb to Pericentric Heterochromatin in Embryonic Stem Cells Reveals a Role for H2AK119u1 in PRC2 Recruitment
journal, June 2014


Multifunctional nascent polypeptide-associated complex (NAC)
journal, March 2014


Next-generation sequencing to generate interactome datasets
journal, April 2011

  • Yu, Haiyuan; Tardivo, Leah; Tam, Stanley
  • Nature Methods, Vol. 8, Issue 6
  • DOI: 10.1038/nmeth.1597

POFs: what we don’t know can hurt us
journal, November 2007


Phylogeny.fr: robust phylogenetic analysis for the non-specialist
journal, May 2008

  • Dereeper, A.; Guignon, V.; Blanc, G.
  • Nucleic Acids Research, Vol. 36, Issue Web Server
  • DOI: 10.1093/nar/gkn180

Differentially expressed late constituents of the epidermal cornified envelope
journal, November 2001

  • Marshall, D.; Hardman, M. J.; Nield, K. M.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 23
  • DOI: 10.1073/pnas.231489198

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
journal, September 2003


PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins
journal, March 2007

  • Richardt, Sandra; Lang, Daniel; Reski, Ralf
  • Plant Physiology, Vol. 143, Issue 4
  • DOI: 10.1104/pp.107.095760

Towards revealing the functions of all genes in plants
journal, April 2014


Function of the apetala-1 gene during Arabidopsis floral development.
journal, August 1990


Identification of DNA sequences required for activity of the cauliflower mosaic virus 35S promoter
journal, February 1985

  • Odell, Joan T.; Nagy, Ferenc; Chua, Nam-Hai
  • Nature, Vol. 313, Issue 6005, p. 810-812
  • DOI: 10.1038/313810a0

Repression of gene expression by Arabidopsis HD2 histone deacetylases
journal, April 2003


The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
journal, December 2011

  • Lamesch, Philippe; Berardini, Tanya Z.; Li, Donghui
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1090

Evidence for Network Evolution in an Arabidopsis Interactome Map
journal, July 2011


Synergistic use of plant-prokaryote comparative genomics for functional annotations
journal, January 2011


Noncoding RNA and Polycomb recruitment
journal, February 2013


Tug of war: adding and removing histone lysine methylation in Arabidopsis
journal, December 2016


AGRIS: the Arabidopsis Gene Regulatory Information Server, an update
journal, November 2010

  • Yilmaz, A.; Mejia-Guerra, M. K.; Kurz, K.
  • Nucleic Acids Research, Vol. 39, Issue Database
  • DOI: 10.1093/nar/gkq1120

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
journal, January 2010

  • Lee, Insuk; Ambaru, Bindu; Thakkar, Pranjali
  • Nature Biotechnology, Vol. 28, Issue 2
  • DOI: 10.1038/nbt.1603

Transcription-associated protein families are primarily taxon-specific
journal, January 2001


The Arabidopsis Chaperone J3 Regulates the Plasma Membrane H + -ATPase through Interaction with the PKS5 Kinase
journal, April 2010


Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources
journal, May 2012


Recruitment of the Mammalian Histone-modifying EMSY Complex to Target Genes Is Regulated by ZNF131
journal, February 2016

  • Varier, Radhika A.; de Santa Pau, Enrique Carrillo; van der Groep, Petra
  • Journal of Biological Chemistry, Vol. 291, Issue 14
  • DOI: 10.1074/jbc.M115.701227

Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation
journal, July 2007

  • Nakagawa, Tsuyoshi; Kurose, Takayuki; Hino, Takeshi
  • Journal of Bioscience and Bioengineering, Vol. 104, Issue 1
  • DOI: 10.1263/jbb.104.34

Identification and Characterization of a Novel Nuclear Protein Complex Involved in Nuclear Hormone Receptor-mediated Gene Regulation
journal, January 2009

  • Garapaty, Shivani; Xu, Chong-Feng; Trojer, Patrick
  • Journal of Biological Chemistry, Vol. 284, Issue 12
  • DOI: 10.1074/jbc.M805872200

Expanding functional diversity of the coactivators
journal, March 2005


Dual-function transcription factors and their entourage: Unique and unifying themes governing two pathogenesis-related genes
journal, June 2010

  • Boyle, Patrick; Després, Charles
  • Plant Signaling & Behavior, Vol. 5, Issue 6
  • DOI: 10.4161/psb.5.6.11570

YLoc—an interpretable web server for predicting subcellular localization
journal, May 2010

  • Briesemeister, Sebastian; Rahnenf�hrer, J�rg; Kohlbacher, Oliver
  • Nucleic Acids Research, Vol. 38, Issue suppl_2
  • DOI: 10.1093/nar/gkq477

Large-scale analysis of the GRAS gene family in Arabidopsis thaliana
journal, May 2008


Intrinsically disordered proteins: a 10-year recap
journal, December 2012


TMC1 and TMC2 Are Components of the Mechanotransduction Channel in Hair Cells of the Mammalian Inner Ear
journal, August 2013


Saccharomyces Genome Database: the genomics resource of budding yeast
journal, November 2011

  • Cherry, J. M.; Hong, E. L.; Amundsen, C.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1029

Recruiting polycomb to chromatin
journal, October 2015

  • van Kruijsbergen, Ila; Hontelez, Saartje; Veenstra, Gert Jan C.
  • The International Journal of Biochemistry & Cell Biology, Vol. 67
  • DOI: 10.1016/j.biocel.2015.05.006

The COMPASS Family of H3K4 Methylases in Drosophila
journal, August 2011

  • Mohan, M.; Herz, H. -M.; Smith, E. R.
  • Molecular and Cellular Biology, Vol. 31, Issue 21
  • DOI: 10.1128/MCB.06092-11

The Polycomb Group Protein Regulatory Network
journal, April 2015


Within leaf variation is the largest source of variation in agroinfiltration of Nicotiana benthamiana
journal, October 2015


Why Are There Still Over 1000 Uncharacterized Yeast Genes?
journal, April 2007


Intrinsic Disorder in Transcription Factors
journal, June 2006

  • Liu, Jiangang; Perumal, Narayanan B.; Oldfield, Christopher J.
  • Biochemistry, Vol. 45, Issue 22
  • DOI: 10.1021/bi0602718

    Works referencing / citing this record:

    Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction [Supplemental Data]
    dataset, June 2017

    • Bossi, Flavia; Fan, Jue; Xiao, Jun
    • figshare-Supplementary information for journal article at DOI: 10.1186/s12864-017-3853-9, 1 DOCX file (1.73 MB)
    • DOI: 10.6084/m9.figshare.c.3811804

    Additional file 1: of Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction [Supplemental Data]
    dataset, June 2017

    • Bossi, Flavia; Fan, Jue; Xiao, Jun
    • figshare-Supplementary information for journal article at DOI: 10.1186/s12864-017-3853-9, 1 DOCX file; 1.73 MB
    • DOI: 10.6084/m9.figshare.c.3811804_d1

      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.