Additional file 2: of Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data

Additional file 2: of Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines

Jiayue-Clara Jiang (6642887)
Kyle Upton (3587213)

April 2019

CAGE clusters and genes mapped to putative TE-derived promoters: contains the list of CAGE clusters ...

Additional file 3: of A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions

Katrin Sameith (3583766)
Saman Amini (3583751)
Marian Groot Koerkamp (3583754)
Dik van Leenen (68452)
Mariel Brok (3583772)
Nathalie Brabers (133205)
Philip Lijnzaad (25992)
Sander van Hooff (133215)
Joris Benschop (3583748)
Tineke Lenstra (3583757)
Eva Apweiler (3583769)
Sake van Wageningen (3583763)
Berend Snel (5539)
Frank Holstege (3583760)
Patrick Kemmeren (492813)

December 2015

Contribution of selection criteria to genetic interaction types. (A) Hierarchical clustering of GSTF...

Additional file 3 of Thirty biologically interpretable clusters of transcription factors distinguish cancer type

Zachary B. Abrams (4745061)
Mark Zucker (5845352)
Min Wang (21070)
Amir Asiaee Taheri (5845355)
Lynne V. Abruzzo (194625)
Kevin R. Coombes (160319)

October 2018

Results of ToppGene analysis of each of the thirty biological components. (XLSX 571 kb

Additional file 3: of Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data

Ruimin Wang (317092)
Yunlong Wang (180471)
Xueying Zhang (460267)
Yaliang Zhang (6678452)
Xiaoyong Du (1865638)
Yaping Fang (131564)
Guoliang Li (131171)

May 2019

Supporting figures. Figure S1. Hierarchical structures of the GM12878 TFs network. Figure S2. Percen...

Additional file 2: of Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors

Xiaoyan Ma (205032)
Daphne Ezer (3072147)
Boris Adryan (31888)
Tim Stevens (3233313)

October 2018

Figure S1. Further dissection of TF site occupancy and spatial co-localization. Figure S2. The relat...

Additional file 5: of Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data

Ruimin Wang (317092)
Yunlong Wang (180471)
Xueying Zhang (460267)
Yaliang Zhang (6678452)
Xiaoyong Du (1865638)
Yaping Fang (131564)
Guoliang Li (131171)

May 2019

The biclustering results of cliques and genes. We adopt the 51 cliques and 1223 regulated genes of K...

Additional file 1: of Revealing transcription factor and histone modification co-localization and dynamics across cell lines by integrating ChIP-seq and RNA-seq data

Lirong Zhang (391975)
Gaogao Xue (6167855)
Junjie Liu (193511)
Qianzhong Li (3623429)
Yong Wang (12837)

January 2019

Table S1. The brief introduction of two cell lines. Table S2. Transcription factors associated with ...

Additional file 1: of Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data

Ruimin Wang (317092)
Yunlong Wang (180471)
Xueying Zhang (460267)
Yaliang Zhang (6678452)
Xiaoyong Du (1865638)
Yaping Fang (131564)
Guoliang Li (131171)

May 2019

All datasets used in this study (ChIA-PET, Chromatin states, TAD structure, and bisulfite-sequencing...

Additional file 2: of Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization

Saskia Trescher (3864526)
Jannes Münchmeyer (3864568)
Ulf Leser (7906)

March 2017

Includes an adjacency list of the connected nodes of the TF – gene network. The list includes three ...

Additional file 1: of Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors

Xiaoyan Ma (205032)
Daphne Ezer (3072147)
Boris Adryan (31888)
Tim Stevens (3233313)

October 2018

Table S1. Sources for TF binding data. Table S2. Co-localization of lymphoblastoid TF pairs. Table S...

Additional file 1: of Constructing tissue-specific transcriptional regulatory networks via a Markov random field

Shining Ma (6167861)
Tao Jiang (28401)
Rui Jiang (264894)

January 2019

Figure S1. The directed acyclic subgraph of the human cell hierarchical taxonomy graph. Figure S2 Th...

Additional file 2: of Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

A. Barutcu (3490721)
Bryan Lajoie (3481844)
Rachel McCord (3490733)
Coralee Tye (3490730)
Deli Hong (3490739)
Terri Messier (3490724)
Gillian Browne (3490727)
Andre van Wijnen (3476351)
Jane Lian (3490736)
Janet Stein (2267158)
Job Dekker (48174)
Anthony Imbalzano (3490742)
Gary Stein (2267170)

September 2015

A table listing the gene ontology terms of differentially expressed genes between MCF-10A and MCF-7 ...

Additional file 10: Figure S9. of Disrupted cooperation between transcription factors across diverse cancer types

Jing Wang (1228470)
Qi Liu (33068)
Jingchun Sun (40514)
Yu Shyr (28592)

August 2016

Cut-offs for identifying highly dyscooperated TFs. (A) The distribution of the number the Z-transfor...

Additional file 2 of Functional and transcriptional connectivity of communities in breast cancer co-expression networks

Guillermo de Anda-Jáuregui (4902250)
Sergio Antonio Alcalá-Corona (5847176)
Jesús Espinal-Enríquez (622164)
Enrique Hernández-Lemus (286050)

May 2019

Supplementary Data. Excel file with Topological parameters for co-expression networks (TXT 478 b

Additional file 1: Figure S1. of Disrupted cooperation between transcription factors across diverse cancer types

Jing Wang (1228470)
Qi Liu (33068)
Jingchun Sun (40514)
Yu Shyr (28592)

August 2016

The correlation between TF pairs from different datasets. The box plots illustrate the correlation (...

Additional file 2: of Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines

Jiayue-Clara Jiang (6642887)
Kyle Upton (3587213)

April 2019

CAGE clusters and genes mapped to putative TE-derived promoters: contains the list of CAGE clusters ...

Additional file 3: of A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions

Katrin Sameith (3583766)
Saman Amini (3583751)
Marian Groot Koerkamp (3583754)
Dik van Leenen (68452)
Mariel Brok (3583772)
Nathalie Brabers (133205)
Philip Lijnzaad (25992)
Sander van Hooff (133215)
Joris Benschop (3583748)
Tineke Lenstra (3583757)
Eva Apweiler (3583769)
Sake van Wageningen (3583763)
Berend Snel (5539)
Frank Holstege (3583760)
Patrick Kemmeren (492813)

December 2015

Contribution of selection criteria to genetic interaction types. (A) Hierarchical clustering of GSTF...

Additional file 3 of Thirty biologically interpretable clusters of transcription factors distinguish cancer type

Zachary B. Abrams (4745061)
Mark Zucker (5845352)
Min Wang (21070)
Amir Asiaee Taheri (5845355)
Lynne V. Abruzzo (194625)
Kevin R. Coombes (160319)

October 2018

Results of ToppGene analysis of each of the thirty biological components. (XLSX 571 kb

Additional file 3: of Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data

Ruimin Wang (317092)
Yunlong Wang (180471)
Xueying Zhang (460267)
Yaliang Zhang (6678452)
Xiaoyong Du (1865638)
Yaping Fang (131564)
Guoliang Li (131171)

May 2019

Supporting figures. Figure S1. Hierarchical structures of the GM12878 TFs network. Figure S2. Percen...

Additional file 2: of Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors

Xiaoyan Ma (205032)
Daphne Ezer (3072147)
Boris Adryan (31888)
Tim Stevens (3233313)

October 2018

Figure S1. Further dissection of TF site occupancy and spatial co-localization. Figure S2. The relat...

Additional file 5: of Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data

Ruimin Wang (317092)
Yunlong Wang (180471)
Xueying Zhang (460267)
Yaliang Zhang (6678452)
Xiaoyong Du (1865638)
Yaping Fang (131564)
Guoliang Li (131171)

May 2019

The biclustering results of cliques and genes. We adopt the 51 cliques and 1223 regulated genes of K...

Additional file 1: of Revealing transcription factor and histone modification co-localization and dynamics across cell lines by integrating ChIP-seq and RNA-seq data

Lirong Zhang (391975)
Gaogao Xue (6167855)
Junjie Liu (193511)
Qianzhong Li (3623429)
Yong Wang (12837)

January 2019

Table S1. The brief introduction of two cell lines. Table S2. Transcription factors associated with ...

Additional file 1: of Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data

Ruimin Wang (317092)
Yunlong Wang (180471)
Xueying Zhang (460267)
Yaliang Zhang (6678452)
Xiaoyong Du (1865638)
Yaping Fang (131564)
Guoliang Li (131171)

May 2019

All datasets used in this study (ChIA-PET, Chromatin states, TAD structure, and bisulfite-sequencing...

Additional file 2: of Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization

Saskia Trescher (3864526)
Jannes Münchmeyer (3864568)
Ulf Leser (7906)

March 2017

Includes an adjacency list of the connected nodes of the TF – gene network. The list includes three ...

Additional file 1: of Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors

Xiaoyan Ma (205032)
Daphne Ezer (3072147)
Boris Adryan (31888)
Tim Stevens (3233313)

October 2018

Table S1. Sources for TF binding data. Table S2. Co-localization of lymphoblastoid TF pairs. Table S...

Additional file 1: of Constructing tissue-specific transcriptional regulatory networks via a Markov random field

Shining Ma (6167861)
Tao Jiang (28401)
Rui Jiang (264894)

January 2019

Figure S1. The directed acyclic subgraph of the human cell hierarchical taxonomy graph. Figure S2 Th...

Additional file 2: of Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

A. Barutcu (3490721)
Bryan Lajoie (3481844)
Rachel McCord (3490733)
Coralee Tye (3490730)
Deli Hong (3490739)
Terri Messier (3490724)
Gillian Browne (3490727)
Andre van Wijnen (3476351)
Jane Lian (3490736)
Janet Stein (2267158)
Job Dekker (48174)
Anthony Imbalzano (3490742)
Gary Stein (2267170)

September 2015

A table listing the gene ontology terms of differentially expressed genes between MCF-10A and MCF-7 ...

Additional file 10: Figure S9. of Disrupted cooperation between transcription factors across diverse cancer types

Jing Wang (1228470)
Qi Liu (33068)
Jingchun Sun (40514)
Yu Shyr (28592)

August 2016

Cut-offs for identifying highly dyscooperated TFs. (A) The distribution of the number the Z-transfor...

Additional file 2 of Functional and transcriptional connectivity of communities in breast cancer co-expression networks

Guillermo de Anda-Jáuregui (4902250)
Sergio Antonio Alcalá-Corona (5847176)
Jesús Espinal-Enríquez (622164)
Enrique Hernández-Lemus (286050)

May 2019

Supplementary Data. Excel file with Topological parameters for co-expression networks (TXT 478 b

Additional file 1: Figure S1. of Disrupted cooperation between transcription factors across diverse cancer types

Jing Wang (1228470)
Qi Liu (33068)
Jingchun Sun (40514)
Yu Shyr (28592)

August 2016

The correlation between TF pairs from different datasets. The box plots illustrate the correlation (...

Additional file 2: of Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines

Jiayue-Clara Jiang (6642887)
Kyle Upton (3587213)

April 2019

CAGE clusters and genes mapped to putative TE-derived promoters: contains the list of CAGE clusters ...

Additional file 3: of A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions

Katrin Sameith (3583766)
Saman Amini (3583751)
Marian Groot Koerkamp (3583754)
Dik van Leenen (68452)
Mariel Brok (3583772)
Nathalie Brabers (133205)
Philip Lijnzaad (25992)
Sander van Hooff (133215)
Joris Benschop (3583748)
Tineke Lenstra (3583757)
Eva Apweiler (3583769)
Sake van Wageningen (3583763)
Berend Snel (5539)
Frank Holstege (3583760)
Patrick Kemmeren (492813)

December 2015

Contribution of selection criteria to genetic interaction types. (A) Hierarchical clustering of GSTF...

Additional file 3 of Thirty biologically interpretable clusters of transcription factors distinguish cancer type

Zachary B. Abrams (4745061)
Mark Zucker (5845352)
Min Wang (21070)
Amir Asiaee Taheri (5845355)
Lynne V. Abruzzo (194625)
Kevin R. Coombes (160319)

October 2018

Results of ToppGene analysis of each of the thirty biological components. (XLSX 571 kb

Additional file 2: of Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data

Abstract

Extracted data

Additional file 2: of Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data

Abstract

Extracted data

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