Additional file 5: of Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes

Additional file 1: of Using machine learning algorithms to identify genes essential for cell survival

Santosh Philips (4489522)
Heng-Yi Wu (737267)
Lang Li (91927)

October 2017

The file contains three sheets labelled Table S1 - S3. The tables list the genes that are currently ...

Additional file 2: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

Krista Vincent (3576728)
Scott Findlay (3576725)
Lynne Postovit (3576731)

August 2015

Top 1 % of differentially expressed genes between tumours and cell lines (with adjusted p values by ...

Additional file 2: of The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens

Dimitra Repana (6173975)
Joel Nulsen (6173978)
Lisa Dressler (6173981)
Michele Bortolomeazzi (6173984)
Santhilata Venkata (6173987)
Aikaterini Tourna (6173990)
Anna Yakovleva (778118)
Tommaso Palmieri (6173993)
Francesca Ciccarelli (6173996)

January 2019

Table S1. Systems-level properties of cancer genes. Table S2 List of 273 publications describing can...

Additional file 6: of Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes

Hao Cai (1324782)
Xiangyu Li (1475548)
Jun He (46556)
Wenbin Zhou (295899)
Kai Song (107003)
You Guo (4622707)
Huaping Liu (769096)
Qingzhou Guan (3728839)
Haidan Yan (3728836)
Xianlong Wang (432284)
Zheng Guo (14989)

February 2019

Table S3. Pathway enrichment analysis of the absolute DEGs and relative DEGs for ten cancers. (XLSX ...

Additional file 4: of Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes

Hao Cai (1324782)
Xiangyu Li (1475548)
Jun He (46556)
Wenbin Zhou (295899)
Kai Song (107003)
You Guo (4622707)
Huaping Liu (769096)
Qingzhou Guan (3728839)
Haidan Yan (3728836)
Xianlong Wang (432284)
Zheng Guo (14989)

February 2019

The simulation experiments in data with global transcriptome size changes due to the genome size cha...

Additional file 5: of Adaptively capturing the heterogeneity of expression for cancer biomarker identification

Xin-Ping Xie (4383745)
Yu-Feng Xie (4383742)
Yi-Tong Liu (5613974)
Hong-Qiang Wang (475907)

November 2018

Table S4. List of 3548 DEGs identified on the HCC RNA-Seq data set with positive aGRP statistics. (C...

Additional file 7: of Separation of breast cancer and organ microenvironment transcriptomes in metastases

Mohammad Alzubi (6431630)
Tia Turner (6431633)
Amy Olex (6431636)
Sahib Sohal (6431639)
Nicholas Tobin (4848271)
Susana Recio (6431642)
Jonas Bergh (23551)
Thomas Hatschek (22685)
Joel Parker (17174)
Carol Sartorius (6431645)
Charles Perou (3530138)
Mikhail Dozmorov (4630)
J. Harrell (6413768)

March 2019

Genes upregulated during liver metastasis; cancer and organ-specific changes. DESeq2 was used to ide...

Additional file 5: Table S2. of High-throughput mRNA and miRNA profiling of epithelial-mesenchymal transition in MDCK cells

Priyank Shukla (398088)
Claus Vogl (265659)
Barbara Wallner (319223)
Doris Rigler (3476729)
Mathias MĂźller (3476738)
Sabine Macho-Maschler (3476726)

November 2015

RNA-Seq gene counts. Listed are number of genes found and differentially expressed. The numbers of g...

Additional file 5: of CTCF maintains regulatory homeostasis of cancer pathways

Sarah Aitken (5612171)
Ximena Ibarra-Soria (625555)
Elissavet Kentepozidou (5612174)
Paul Flicek (77154)
Christine Feig (5612177)
John Marioni (634806)
Duncan Odom (3534446)

August 2018

Mouse and human tumor metadata and differential expression results of RNA-seq data. Sample informati...

Additional file 9: of Separation of breast cancer and organ microenvironment transcriptomes in metastases

Mohammad Alzubi (6431630)
Tia Turner (6431633)
Amy Olex (6431636)
Sahib Sohal (6431639)
Nicholas Tobin (4848271)
Susana Recio (6431642)
Jonas Bergh (23551)
Thomas Hatschek (22685)
Joel Parker (17174)
Carol Sartorius (6431645)
Charles Perou (3530138)
Mikhail Dozmorov (4630)
J. Harrell (6413768)

March 2019

Genes upregulated during lung metastasis; cancer and organ-specific changes. DESeq2 was used to iden...

Additional file 2: of Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

Tianyu Wang (397547)
Boyang Li (4268965)
Craig Nelson (3498350)
Sheida Nabavi (3493139)

January 2019

Results of the Gene Ontology Process enrichment analysis of the 300 top-ranked DE genes and the list...

Additional file 2: Table S2. of Identification of mRNA isoform switching in breast cancer

Wei Zhao (14321)
Katherine Hoadley (3530135)
Joel Parker (17174)
Charles Perou (3530138)

March 2016

43 genes with more than 10 expressed and detected transcripts per gene. (XLSX 10 kb

Additional file 1: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

Zhuyi Xue (5514434)
René Warren (5431511)
Ewan Gibb (5514431)
Daniel MacMillan (5514440)
Johnathan Wong (5514425)
Readman Chiu (41422)
S. Austin Hammond (762521)
Chen Yang (207381)
Ka Nip (5514428)
Catherine Ennis (5514437)
Abigail Hahn (5514422)
Sheila Reynolds (4693027)
Inanc Birol (277074)

July 2018

Supplementary figures. It includes all supplementary figures except Figure S4. Figure S1. Benchmark ...

Additional file 5: of Feature selection of gene expression data for Cancer classification using double RBF-kernels

Shenghui Liu (5210906)
Chunrui Xu (5907374)
Yusen Zhang (656232)
Jiaguo Liu (843490)
Bin Yu (14464)
Xiaoping Liu (240534)
Matthias Dehmer (95417)

October 2018

top-50 gene expression. Figure S1. First fifty top-ranked gene expression level by different methods...

Additional file 2: of The hyper-activation of transcriptional enhancers in breast cancer

Qing-Lan Li (1344414)
Dan-Ya Wang (6456284)
Lin-Gao Ju (6456287)
Jie Yao (1440151)
Chuan Gao (38049)
Pin-Ji Lei (681939)
Lian-Yun Li (681943)
Xiao-Lu Zhao (6456290)
Min Wu (41570)

March 2019

Table S1. List of the relative abundance of all histone peptides. Table S2. List of the relative abu...

Additional file 1: of Using machine learning algorithms to identify genes essential for cell survival

Santosh Philips (4489522)
Heng-Yi Wu (737267)
Lang Li (91927)

October 2017

The file contains three sheets labelled Table S1 - S3. The tables list the genes that are currently ...

Additional file 2: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

Krista Vincent (3576728)
Scott Findlay (3576725)
Lynne Postovit (3576731)

August 2015

Top 1 % of differentially expressed genes between tumours and cell lines (with adjusted p values by ...

Additional file 2: of The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens

Dimitra Repana (6173975)
Joel Nulsen (6173978)
Lisa Dressler (6173981)
Michele Bortolomeazzi (6173984)
Santhilata Venkata (6173987)
Aikaterini Tourna (6173990)
Anna Yakovleva (778118)
Tommaso Palmieri (6173993)
Francesca Ciccarelli (6173996)

January 2019

Table S1. Systems-level properties of cancer genes. Table S2 List of 273 publications describing can...

Additional file 6: of Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes

Hao Cai (1324782)
Xiangyu Li (1475548)
Jun He (46556)
Wenbin Zhou (295899)
Kai Song (107003)
You Guo (4622707)
Huaping Liu (769096)
Qingzhou Guan (3728839)
Haidan Yan (3728836)
Xianlong Wang (432284)
Zheng Guo (14989)

February 2019

Table S3. Pathway enrichment analysis of the absolute DEGs and relative DEGs for ten cancers. (XLSX ...

Additional file 4: of Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes

Hao Cai (1324782)
Xiangyu Li (1475548)
Jun He (46556)
Wenbin Zhou (295899)
Kai Song (107003)
You Guo (4622707)
Huaping Liu (769096)
Qingzhou Guan (3728839)
Haidan Yan (3728836)
Xianlong Wang (432284)
Zheng Guo (14989)

February 2019

The simulation experiments in data with global transcriptome size changes due to the genome size cha...

Additional file 5: of Adaptively capturing the heterogeneity of expression for cancer biomarker identification

Xin-Ping Xie (4383745)
Yu-Feng Xie (4383742)
Yi-Tong Liu (5613974)
Hong-Qiang Wang (475907)

November 2018

Table S4. List of 3548 DEGs identified on the HCC RNA-Seq data set with positive aGRP statistics. (C...

Additional file 7: of Separation of breast cancer and organ microenvironment transcriptomes in metastases

Mohammad Alzubi (6431630)
Tia Turner (6431633)
Amy Olex (6431636)
Sahib Sohal (6431639)
Nicholas Tobin (4848271)
Susana Recio (6431642)
Jonas Bergh (23551)
Thomas Hatschek (22685)
Joel Parker (17174)
Carol Sartorius (6431645)
Charles Perou (3530138)
Mikhail Dozmorov (4630)
J. Harrell (6413768)

March 2019

Genes upregulated during liver metastasis; cancer and organ-specific changes. DESeq2 was used to ide...

Additional file 5: Table S2. of High-throughput mRNA and miRNA profiling of epithelial-mesenchymal transition in MDCK cells

Priyank Shukla (398088)
Claus Vogl (265659)
Barbara Wallner (319223)
Doris Rigler (3476729)
Mathias MĂźller (3476738)
Sabine Macho-Maschler (3476726)

November 2015

RNA-Seq gene counts. Listed are number of genes found and differentially expressed. The numbers of g...

Additional file 5: of CTCF maintains regulatory homeostasis of cancer pathways

Sarah Aitken (5612171)
Ximena Ibarra-Soria (625555)
Elissavet Kentepozidou (5612174)
Paul Flicek (77154)
Christine Feig (5612177)
John Marioni (634806)
Duncan Odom (3534446)

August 2018

Mouse and human tumor metadata and differential expression results of RNA-seq data. Sample informati...

Additional file 9: of Separation of breast cancer and organ microenvironment transcriptomes in metastases

Mohammad Alzubi (6431630)
Tia Turner (6431633)
Amy Olex (6431636)
Sahib Sohal (6431639)
Nicholas Tobin (4848271)
Susana Recio (6431642)
Jonas Bergh (23551)
Thomas Hatschek (22685)
Joel Parker (17174)
Carol Sartorius (6431645)
Charles Perou (3530138)
Mikhail Dozmorov (4630)
J. Harrell (6413768)

March 2019

Genes upregulated during lung metastasis; cancer and organ-specific changes. DESeq2 was used to iden...

Additional file 2: of Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

Tianyu Wang (397547)
Boyang Li (4268965)
Craig Nelson (3498350)
Sheida Nabavi (3493139)

January 2019

Results of the Gene Ontology Process enrichment analysis of the 300 top-ranked DE genes and the list...

Additional file 2: Table S2. of Identification of mRNA isoform switching in breast cancer

Wei Zhao (14321)
Katherine Hoadley (3530135)
Joel Parker (17174)
Charles Perou (3530138)

March 2016

43 genes with more than 10 expressed and detected transcripts per gene. (XLSX 10 kb

Additional file 1: of Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

Zhuyi Xue (5514434)
René Warren (5431511)
Ewan Gibb (5514431)
Daniel MacMillan (5514440)
Johnathan Wong (5514425)
Readman Chiu (41422)
S. Austin Hammond (762521)
Chen Yang (207381)
Ka Nip (5514428)
Catherine Ennis (5514437)
Abigail Hahn (5514422)
Sheila Reynolds (4693027)
Inanc Birol (277074)

July 2018

Supplementary figures. It includes all supplementary figures except Figure S4. Figure S1. Benchmark ...

Additional file 5: of Feature selection of gene expression data for Cancer classification using double RBF-kernels

Shenghui Liu (5210906)
Chunrui Xu (5907374)
Yusen Zhang (656232)
Jiaguo Liu (843490)
Bin Yu (14464)
Xiaoping Liu (240534)
Matthias Dehmer (95417)

October 2018

top-50 gene expression. Figure S1. First fifty top-ranked gene expression level by different methods...

Additional file 2: of The hyper-activation of transcriptional enhancers in breast cancer

Qing-Lan Li (1344414)
Dan-Ya Wang (6456284)
Lin-Gao Ju (6456287)
Jie Yao (1440151)
Chuan Gao (38049)
Pin-Ji Lei (681939)
Lian-Yun Li (681943)
Xiao-Lu Zhao (6456290)
Min Wu (41570)

March 2019

Table S1. List of the relative abundance of all histone peptides. Table S2. List of the relative abu...

Additional file 1: of Using machine learning algorithms to identify genes essential for cell survival

Santosh Philips (4489522)
Heng-Yi Wu (737267)
Lang Li (91927)

October 2017

The file contains three sheets labelled Table S1 - S3. The tables list the genes that are currently ...

Additional file 2: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

Krista Vincent (3576728)
Scott Findlay (3576725)
Lynne Postovit (3576731)

August 2015

Top 1 % of differentially expressed genes between tumours and cell lines (with adjusted p values by ...

Additional file 2: of The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens

Dimitra Repana (6173975)
Joel Nulsen (6173978)
Lisa Dressler (6173981)
Michele Bortolomeazzi (6173984)
Santhilata Venkata (6173987)
Aikaterini Tourna (6173990)
Anna Yakovleva (778118)
Tommaso Palmieri (6173993)
Francesca Ciccarelli (6173996)

January 2019

Table S1. Systems-level properties of cancer genes. Table S2 List of 273 publications describing can...

Additional file 5: of Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes

Abstract

Extracted data

Additional file 5: of Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes

Abstract

Extracted data

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