Published online 29 December 2016
Nucleic Acids Research, 2017, Vol. 45, No. 9 5625–5626 doi: 10.1093/nar/gkw1342
Corrigendum ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium Qi You1 , Wenying Xu1 , Kang Zhang1 , Liwei Zhang1 , Xin Yi1 , Dongxia Yao1 , Chunchao Wang1 , Xueyan Zhang2 , Xinhua Zhao2 , Nicholas J. Provart3 , Fuguang Li2,* and Zhen Su1,* 1
State key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China, 2 State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agriculture Sciences (CAAS), Anyang, Henan 455000, China and 3 Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St, Toronto, ON M5S 3B2, Canada
Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw910 The authors wish to draw attention to an error in their published article. The original Table 1 is not correct due to the error numbers for ‘Orthologous pairs’ and ‘Comparison sub-networks’. The corrected Table 1 is shown below (updated numbers in bold): Table 1. Collection, prediction and analyses results in ccNET Database content
G. arboreum
G. hirsutum
Reference
Co-expression nodes Positive co-expression edges Positive co-expression edges Tissue-preferential network
33 413 (80.8%) 338 049 207 938 seedling, seed, root, leaf, stem, fiber
(11,49-52)
Stress-response network Protein-protein interaction (nodes/edges) Co-expression function modules (>3 nodes overlap) miRNA target modules Orthologous pairs (genes in each species) Comparison sub-networks (> 3 orthologous pairs) GO annotation entries (genes) KEGG pathways (genes) Transcription regulators (families) Kinases (families) Carbohydrate-active enzymes Cis-elements (kinds of existed motifs) H3K4me3 modification profiling
NaCl, PEG 18 004/338 863 1155 (493) 213 96 466 (32 417) 85 695 (5718) 72 812 (22 938) 188 (6164) 3305 (81) 1598 (87) 1604 (94) 742 root
65 870 (93.4%) 593 758 291 801 root, stem, leaf, cotyledon, calycle, petal, torus, stamen, ovule, pistil, seed Salt, PEG, Cold, Hot 27 422/696 090 1884 (1080) 135 96 466 (62 050) 85 695 (5718) 119 867 (41 939) 391 (36 934) 6422 (81) 2999 (87) 2719 (95) 747 root
(11,51) (14,18-23) (32,33) (34-37) (17) (17) (39) (40) (41) (24-30) -
The first sentence in the section ‘Comparison between diploid and allotetraploid cotton’ should be replaced with: * To
whom correspondence should be addressed. Tel: +86 10 62731380; Fax: +86 10 62731380; Email: [email protected] Correspondence may also be addressed to Fuguang Li. Tel: +86 372 2562256; Fax: +86 372 2562256; Email: [email protected]
C The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected]
5626 Nucleic Acids Research, 2017, Vol. 45, No. 9
“In total, 96 466 ortholog pairs in 16 142 homologous groups, including 32 417 (78.4% coverage) and 62 050 (88.0% coverage) genes in G. arboreum and G. hirsutum, respectively, have been established through a bidirectional BLAST algorithm-based alignment and strict E-value cutoff (1E-55) (31).” The Authors apologise to the Readers for these errors. REFERENCE 31. Zhang,L., Guo,J., You,Q., Yi,X., Ling,Y., Xu,W., Hua,J. and Su,Z. (2015) GraP: Platform for functional genomics analysis of Gossypium raimondii. Database (Oxford), bav047.
Nucleic Acids Research, 2017, Vol. 45, No. 9 5625–5626 doi: 10.1093/nar/gkw1342
Corrigendum ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium Qi You1 , Wenying Xu1 , Kang Zhang1 , Liwei Zhang1 , Xin Yi1 , Dongxia Yao1 , Chunchao Wang1 , Xueyan Zhang2 , Xinhua Zhao2 , Nicholas J. Provart3 , Fuguang Li2,* and Zhen Su1,* 1
State key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China, 2 State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agriculture Sciences (CAAS), Anyang, Henan 455000, China and 3 Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St, Toronto, ON M5S 3B2, Canada
Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw910 The authors wish to draw attention to an error in their published article. The original Table 1 is not correct due to the error numbers for ‘Orthologous pairs’ and ‘Comparison sub-networks’. The corrected Table 1 is shown below (updated numbers in bold): Table 1. Collection, prediction and analyses results in ccNET Database content
G. arboreum
G. hirsutum
Reference
Co-expression nodes Positive co-expression edges Positive co-expression edges Tissue-preferential network
33 413 (80.8%) 338 049 207 938 seedling, seed, root, leaf, stem, fiber
(11,49-52)
Stress-response network Protein-protein interaction (nodes/edges) Co-expression function modules (>3 nodes overlap) miRNA target modules Orthologous pairs (genes in each species) Comparison sub-networks (> 3 orthologous pairs) GO annotation entries (genes) KEGG pathways (genes) Transcription regulators (families) Kinases (families) Carbohydrate-active enzymes Cis-elements (kinds of existed motifs) H3K4me3 modification profiling
NaCl, PEG 18 004/338 863 1155 (493) 213 96 466 (32 417) 85 695 (5718) 72 812 (22 938) 188 (6164) 3305 (81) 1598 (87) 1604 (94) 742 root
65 870 (93.4%) 593 758 291 801 root, stem, leaf, cotyledon, calycle, petal, torus, stamen, ovule, pistil, seed Salt, PEG, Cold, Hot 27 422/696 090 1884 (1080) 135 96 466 (62 050) 85 695 (5718) 119 867 (41 939) 391 (36 934) 6422 (81) 2999 (87) 2719 (95) 747 root
(11,51) (14,18-23) (32,33) (34-37) (17) (17) (39) (40) (41) (24-30) -
The first sentence in the section ‘Comparison between diploid and allotetraploid cotton’ should be replaced with: * To
whom correspondence should be addressed. Tel: +86 10 62731380; Fax: +86 10 62731380; Email: [email protected] Correspondence may also be addressed to Fuguang Li. Tel: +86 372 2562256; Fax: +86 372 2562256; Email: [email protected]
C The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected]
5626 Nucleic Acids Research, 2017, Vol. 45, No. 9
“In total, 96 466 ortholog pairs in 16 142 homologous groups, including 32 417 (78.4% coverage) and 62 050 (88.0% coverage) genes in G. arboreum and G. hirsutum, respectively, have been established through a bidirectional BLAST algorithm-based alignment and strict E-value cutoff (1E-55) (31).” The Authors apologise to the Readers for these errors. REFERENCE 31. Zhang,L., Guo,J., You,Q., Yi,X., Ling,Y., Xu,W., Hua,J. and Su,Z. (2015) GraP: Platform for functional genomics analysis of Gossypium raimondii. Database (Oxford), bav047.
