Additional file 13: Table S10. of Histone modifications facilitate the coexpression of bidirectional promoters in rice

Additional file 12: of Comparative functional genomics analysis of bHLH gene family in rice, maize and wheat

Kaifa Wei (594582)
Huiqin Chen (790682)

November 2018

Table S6. The distribution of cis-regulatory elements in TabHLH promoters. âYâ means that the el...

Additional file 6: of Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci

Qiaoqiao Zhu (6682643)
Mukund Ramakrishnan (6682646)
Jinhee Park (672569)
William Belden (5907128)

May 2019

Gene expression clusters of WT, ∆kmt1/∆dim-5 and ∆kmt2/∆set-1. Gene expression patterns were cluster...

Additional file 3: of Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression

Qi Zhang (28502)
Dong-Ha Oh (3504020)
Sandra DiTusa (4802043)
Mangu RamanaRao (4802046)
Niranjan Baisakh (778047)
Maheshi Dassanayake (3504014)
Aaron Smith (610734)

January 2018

Figure S3. Correlations between nucleosome patterns and gene expression. (A) Heatmap of MNase-seq de...

Additional file 8: Table S7. of Histone modifications facilitate the coexpression of bidirectional promoters in rice

Yuan Fang (132924)
Lei Wang (6656)
Ximeng Wang (793633)
Qi You (492233)
Xiucai Pan (3405632)
Jin Xiao (111246)
Xiu-e Wang (3405635)
Yufeng Wu (567558)
Zhen Su (18658)
Wenli Zhang (146408)

September 2016

Fold difference of intensity of histone marks and nucleosome occupancy between bidirectional genes a...

Additional file 14: Figure S4. of Histone modifications facilitate the coexpression of bidirectional promoters in rice

Yuan Fang (132924)
Lei Wang (6656)
Ximeng Wang (793633)
Qi You (492233)
Xiucai Pan (3405632)
Jin Xiao (111246)
Xiu-e Wang (3405635)
Yufeng Wu (567558)
Zhen Su (18658)
Wenli Zhang (146408)

September 2016

Comparison of profiling of nucleosome positioning between BDPs and UDPs. Unidirectional gene control...

Additional file 8: of Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

Rahul Jangid (3446135)
Ashwin Kelkar (256849)
Vijaykumar Muley (5162789)
Sanjeev Galande (254158)

May 2018

Figure S8. H3K36me3 distribution on bidirectional gene with different intergenic region in H1 ES cel...

Additional file 9: of Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

Rahul Jangid (3446135)
Ashwin Kelkar (256849)
Vijaykumar Muley (5162789)
Sanjeev Galande (254158)

May 2018

Expression profile 10 bidirectional gene pairs upon RA mediated differentiation of NT2D-1 cells. The...

Additional file 7: Table S4. of Chromatin states responsible for the regulation of differentially expressed genes under 60Co~Îł ray radiation in rice

Xiucai Pan (3405632)
Yuan Fang (132924)
Xueming Yang (593735)
Dongyang Zheng (4511056)
Lifen Chen (3769015)
Lei Wang (6656)
Jin Xiao (111246)
Xiu-e Wang (3405635)
Kai Wang (21246)
Zhukuan Cheng (45762)
Hengxiu Yu (573567)
Wenli Zhang (146408)

October 2017

The p-value of Wilxcoxon rank-sum test (one side) for each mark distributed across up-regulated gene...

Additional file 3: of Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

Rahul Jangid (3446135)
Ashwin Kelkar (256849)
Vijaykumar Muley (5162789)
Sanjeev Galande (254158)

May 2018

Figure S3. H3K4me3 distribution on bidirectional gene with different intergenic distances in H1 ES c...

Additional file 10: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

Shuaibin Lian (5393588)
Tianliang Liu (5393585)
Shengli Jing (574997)
Hongyu Yuan (713804)
Zaibao Zhang (3295551)
Lin Cheng (107461)

June 2018

Figure S2. The histone modification levels of coexpressed gene pairs with three different kinds of c...

Additional file 4: of Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

Rahul Jangid (3446135)
Ashwin Kelkar (256849)
Vijaykumar Muley (5162789)
Sanjeev Galande (254158)

May 2018

Figure S4. H3K4me3 distribution on bidirectional gene with different intergenic region in CD4+ T cel...

Additional file 9: Table S5. of Chromatin states responsible for the regulation of differentially expressed genes under 60Co~Îł ray radiation in rice

Xiucai Pan (3405632)
Yuan Fang (132924)
Xueming Yang (593735)
Dongyang Zheng (4511056)
Lifen Chen (3769015)
Lei Wang (6656)
Jin Xiao (111246)
Xiu-e Wang (3405635)
Kai Wang (21246)
Zhukuan Cheng (45762)
Hengxiu Yu (573567)
Wenli Zhang (146408)

October 2017

The p-value of Wilxcoxon rank-sum test (one side) for each mark distributed across down-regulated ge...

Additional file 13: of Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa

Weiwen Kong (748538)
Li Ding (16240)
Jia Cheng (524760)
Bin Wang (30851)

September 2018

Table S11. The enrichment analysis of the differentially expressed rice genes driven by PIPs through...

Additional file 1: of Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

Rahul Jangid (3446135)
Ashwin Kelkar (256849)
Vijaykumar Muley (5162789)
Sanjeev Galande (254158)

May 2018

Figure S1. Design of dual reporter vector and bidirectional transcription from bidirectional promote...

Additional file 2: of Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

Rahul Jangid (3446135)
Ashwin Kelkar (256849)
Vijaykumar Muley (5162789)
Sanjeev Galande (254158)

May 2018

Figure S2. Characterization of the bidirectional gene pair NFYA-OARD1. (A) The figure shows relative...

Additional file 12: of Comparative functional genomics analysis of bHLH gene family in rice, maize and wheat

Kaifa Wei (594582)
Huiqin Chen (790682)

November 2018

Table S6. The distribution of cis-regulatory elements in TabHLH promoters. âYâ means that the el...

Additional file 6: of Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci

Qiaoqiao Zhu (6682643)
Mukund Ramakrishnan (6682646)
Jinhee Park (672569)
William Belden (5907128)

May 2019

Gene expression clusters of WT, ∆kmt1/∆dim-5 and ∆kmt2/∆set-1. Gene expression patterns were cluster...

Additional file 3: of Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression

Qi Zhang (28502)
Dong-Ha Oh (3504020)
Sandra DiTusa (4802043)
Mangu RamanaRao (4802046)
Niranjan Baisakh (778047)
Maheshi Dassanayake (3504014)
Aaron Smith (610734)

January 2018

Figure S3. Correlations between nucleosome patterns and gene expression. (A) Heatmap of MNase-seq de...

Additional file 8: Table S7. of Histone modifications facilitate the coexpression of bidirectional promoters in rice

Yuan Fang (132924)
Lei Wang (6656)
Ximeng Wang (793633)
Qi You (492233)
Xiucai Pan (3405632)
Jin Xiao (111246)
Xiu-e Wang (3405635)
Yufeng Wu (567558)
Zhen Su (18658)
Wenli Zhang (146408)

September 2016

Fold difference of intensity of histone marks and nucleosome occupancy between bidirectional genes a...

Additional file 14: Figure S4. of Histone modifications facilitate the coexpression of bidirectional promoters in rice

Yuan Fang (132924)
Lei Wang (6656)
Ximeng Wang (793633)
Qi You (492233)
Xiucai Pan (3405632)
Jin Xiao (111246)
Xiu-e Wang (3405635)
Yufeng Wu (567558)
Zhen Su (18658)
Wenli Zhang (146408)

September 2016

Comparison of profiling of nucleosome positioning between BDPs and UDPs. Unidirectional gene control...

Additional file 8: of Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

Rahul Jangid (3446135)
Ashwin Kelkar (256849)
Vijaykumar Muley (5162789)
Sanjeev Galande (254158)

May 2018

Figure S8. H3K36me3 distribution on bidirectional gene with different intergenic region in H1 ES cel...

Additional file 9: of Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

Rahul Jangid (3446135)
Ashwin Kelkar (256849)
Vijaykumar Muley (5162789)
Sanjeev Galande (254158)

May 2018

Expression profile 10 bidirectional gene pairs upon RA mediated differentiation of NT2D-1 cells. The...

Additional file 7: Table S4. of Chromatin states responsible for the regulation of differentially expressed genes under 60Co~Îł ray radiation in rice

Xiucai Pan (3405632)
Yuan Fang (132924)
Xueming Yang (593735)
Dongyang Zheng (4511056)
Lifen Chen (3769015)
Lei Wang (6656)
Jin Xiao (111246)
Xiu-e Wang (3405635)
Kai Wang (21246)
Zhukuan Cheng (45762)
Hengxiu Yu (573567)
Wenli Zhang (146408)

October 2017

The p-value of Wilxcoxon rank-sum test (one side) for each mark distributed across up-regulated gene...

Additional file 3: of Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

Rahul Jangid (3446135)
Ashwin Kelkar (256849)
Vijaykumar Muley (5162789)
Sanjeev Galande (254158)

May 2018

Figure S3. H3K4me3 distribution on bidirectional gene with different intergenic distances in H1 ES c...

Additional file 10: of Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes

Shuaibin Lian (5393588)
Tianliang Liu (5393585)
Shengli Jing (574997)
Hongyu Yuan (713804)
Zaibao Zhang (3295551)
Lin Cheng (107461)

June 2018

Figure S2. The histone modification levels of coexpressed gene pairs with three different kinds of c...

Additional file 4: of Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

Rahul Jangid (3446135)
Ashwin Kelkar (256849)
Vijaykumar Muley (5162789)
Sanjeev Galande (254158)

May 2018

Figure S4. H3K4me3 distribution on bidirectional gene with different intergenic region in CD4+ T cel...

Additional file 9: Table S5. of Chromatin states responsible for the regulation of differentially expressed genes under 60Co~Îł ray radiation in rice

Xiucai Pan (3405632)
Yuan Fang (132924)
Xueming Yang (593735)
Dongyang Zheng (4511056)
Lifen Chen (3769015)
Lei Wang (6656)
Jin Xiao (111246)
Xiu-e Wang (3405635)
Kai Wang (21246)
Zhukuan Cheng (45762)
Hengxiu Yu (573567)
Wenli Zhang (146408)

October 2017

The p-value of Wilxcoxon rank-sum test (one side) for each mark distributed across down-regulated ge...

Additional file 13: of Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa

Weiwen Kong (748538)
Li Ding (16240)
Jia Cheng (524760)
Bin Wang (30851)

September 2018

Table S11. The enrichment analysis of the differentially expressed rice genes driven by PIPs through...

Additional file 1: of Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

Rahul Jangid (3446135)
Ashwin Kelkar (256849)
Vijaykumar Muley (5162789)
Sanjeev Galande (254158)

May 2018

Figure S1. Design of dual reporter vector and bidirectional transcription from bidirectional promote...

Additional file 2: of Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

Rahul Jangid (3446135)
Ashwin Kelkar (256849)
Vijaykumar Muley (5162789)
Sanjeev Galande (254158)

May 2018

Figure S2. Characterization of the bidirectional gene pair NFYA-OARD1. (A) The figure shows relative...

Additional file 12: of Comparative functional genomics analysis of bHLH gene family in rice, maize and wheat

Kaifa Wei (594582)
Huiqin Chen (790682)

November 2018

Table S6. The distribution of cis-regulatory elements in TabHLH promoters. âYâ means that the el...

Additional file 6: of Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci

Qiaoqiao Zhu (6682643)
Mukund Ramakrishnan (6682646)
Jinhee Park (672569)
William Belden (5907128)

May 2019

Gene expression clusters of WT, ∆kmt1/∆dim-5 and ∆kmt2/∆set-1. Gene expression patterns were cluster...

Additional file 3: of Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression

Qi Zhang (28502)
Dong-Ha Oh (3504020)
Sandra DiTusa (4802043)
Mangu RamanaRao (4802046)
Niranjan Baisakh (778047)
Maheshi Dassanayake (3504014)
Aaron Smith (610734)

January 2018

Figure S3. Correlations between nucleosome patterns and gene expression. (A) Heatmap of MNase-seq de...

Additional file 13: Table S10. of Histone modifications facilitate the coexpression of bidirectional promoters in rice

Abstract

Extracted data

Additional file 13: Table S10. of Histone modifications facilitate the coexpression of bidirectional promoters in rice

Abstract

Extracted data

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