Additional file 6: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

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 4 of A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping

Qing Wen (808516)
Chang-Sik Kim (3045420)
Peter Hamilton (438342)
Shu-Dong Zhang (231229)

May 2016

Breast cancer gene signature. The full list of 232 genes (probesets) and their ranks for the optimal...

Additional file 1: of lncRNA SNHG6 regulates EZH2 expression by sponging miR-26a/b and miR-214 in colorectal cancer

Mu Xu (594466)
Xiaoxiang Chen (730749)
Kang Lin (5530313)
Kaixuan Zeng (5802707)
Xiangxiang Liu (617225)
Xueni Xu (5802710)
Bei Pan (5560136)
Tao Xu (3537)
Li Sun (4624)
Bangshun He (119526)
Yuqin Pan (119528)
Huiling Sun (530956)
Shukui Wang (119550)

January 2019

Table S1. The list of primers and probes. Table S2. SiRNAs and sh-RNAs sequence. Table S3. Informati...

Additional file 4: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Feng Liang (447805)
Hongzhu Qu (36515)
Qiang Lin (208776)
Yadong Yang (396824)
Xiuyan Ruan (3450233)
Bo Zhang (6559)
Yi Liu (36759)
Chengze Yu (3450230)
Hongyan Zhang (618068)
Xiangdong Fang (180671)
Xiaopeng Hao (1644652)

August 2015

Classification of genes based on the expression levels. A table showing how the gene expression leve...

Additional file 7: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Feng Liang (447805)
Hongzhu Qu (36515)
Qiang Lin (208776)
Yadong Yang (396824)
Xiuyan Ruan (3450233)
Bo Zhang (6559)
Yi Liu (36759)
Chengze Yu (3450230)
Hongyan Zhang (618068)
Xiangdong Fang (180671)
Xiaopeng Hao (1644652)

August 2015

A KEGG pathway figure for the enriched pathway B cell receptor signaling pathway in down-regulated g...

Additional file 3: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Feng Liang (447805)
Hongzhu Qu (36515)
Qiang Lin (208776)
Yadong Yang (396824)
Xiuyan Ruan (3450233)
Bo Zhang (6559)
Yi Liu (36759)
Chengze Yu (3450230)
Hongyan Zhang (618068)
Xiangdong Fang (180671)
Xiaopeng Hao (1644652)

August 2015

Scatter plots of gene expression values between samples. A figure illustrating how similar of genes ...

Additional file 8: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Feng Liang (447805)
Hongzhu Qu (36515)
Qiang Lin (208776)
Yadong Yang (396824)
Xiuyan Ruan (3450233)
Bo Zhang (6559)
Yi Liu (36759)
Chengze Yu (3450230)
Hongyan Zhang (618068)
Xiangdong Fang (180671)
Xiaopeng Hao (1644652)

August 2015

The schematic diagram of other fused genes. A figure showing how the rest of gene fusions occurred. ...

Additional file 2: of Molecular patterns of cancer colonisation in lymph nodes of breast cancer patients

Gaurav Chatterjee (5998253)
Trupti Pai (5998256)
Thomas Hardiman (5876474)
Kelly Avery-Kiejda (3534812)
Rodney Scott (279337)
Jo Spencer (267903)
Sarah Pinder (553692)
Anita Grigoriadis (41195)

November 2018

Table S2. Genes found to be differentially expressed in multiple studies included in scenario 1 (inv...

Additional file 7: of Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma

Akanksha Verma (3553664)
Yanwen Jiang (103833)
Wei Du (88790)
Lauren Fairchild (3553661)
Ari Melnick (88754)
Olivier Elemento (7617)

November 2015

List of protein-coding genes correlated with lncRNAs. Each protein-coding gene co-expressed with a n...

Additional file 1: of RNA-sequencing in non-small cell lung cancer shows gene downregulation of therapeutic targets in tumor tissue compared to non-malignant lung tissue

Kobe Reynders (5526461)
Els Wauters (101718)
Matthieu Moisse (659185)
Herbert DecaluwĂŠ (5526488)
Paul De Leyn (5526455)
StĂŠphanie Peeters (5526485)
Maarten Lambrecht (5526458)
Kristiaan Nackaerts (3210705)
Christophe Dooms (2938749)
Wim Janssens (101722)
Johan Vansteenkiste (5526467)
Diether Lambrechts (101772)
Dirk De Ruysscher (810406)

July 2018

Table S1. RNA-sequencing results for tumor tissue (a) or non-malignant lung tissue (b). Differential...

Additional file 5: of Molecular patterns of cancer colonisation in lymph nodes of breast cancer patients

Gaurav Chatterjee (5998253)
Trupti Pai (5998256)
Thomas Hardiman (5876474)
Kelly Avery-Kiejda (3534812)
Rodney Scott (279337)
Jo Spencer (267903)
Sarah Pinder (553692)
Anita Grigoriadis (41195)

November 2018

Table S5. Differentially expressed genes representing specific immune cell populations across all th...

Additional file 6: of PLAIDOH: a novel method for functional prediction of long non-coding RNAs identifies cancer-specific LncRNA activities

Sarah Pyfrom (6370442)
Hong Luo (205745)
Jacqueline Payton (6370448)

February 2019

Figure S5. LncRNAs demonstrate common or cancer-type specific positive or negative correlation profi...

Additional file 6: of Mutation status coupled with RNA-sequencing data can efficiently identify important non-significantly mutated genes serving as diagnostic biomarkers of endometrial cancer

Keqin Liu (4725318)
Li He (134049)
Zhichao Liu (191718)
Junmei Xu (4725315)
Yuan Liu (88411)
Qifan Kuang (624438)
Zhining Wen (226349)
Menglong Li (226358)

December 2017

Summary of 1273 non-SMGs showed different expression patterns in the groups of histological type pat...

Additional file 3: Table S2. of Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

M. Ampuja (3631321)
T. Rantapero (3631318)
A. Rodriguez-Martinez (3631312)
M. Palmroth (3631327)
E. Alarmo (3631309)
M. Nykter (3631315)
A. Kallioniemi (3631324)

January 2017

Differentially expressed genes after BMP4 treatment in T-47D cell line. Ensembl IDs, read counts, fo...

Additional file 1: of Molecular patterns of cancer colonisation in lymph nodes of breast cancer patients

Gaurav Chatterjee (5998253)
Trupti Pai (5998256)
Thomas Hardiman (5876474)
Kelly Avery-Kiejda (3534812)
Rodney Scott (279337)
Jo Spencer (267903)
Sarah Pinder (553692)
Anita Grigoriadis (41195)

November 2018

Table S1. Gene list compiled from all the studies included in scenario 1 (involved LN versus primary...

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 4 of A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping

Qing Wen (808516)
Chang-Sik Kim (3045420)
Peter Hamilton (438342)
Shu-Dong Zhang (231229)

May 2016

Breast cancer gene signature. The full list of 232 genes (probesets) and their ranks for the optimal...

Additional file 1: of lncRNA SNHG6 regulates EZH2 expression by sponging miR-26a/b and miR-214 in colorectal cancer

Mu Xu (594466)
Xiaoxiang Chen (730749)
Kang Lin (5530313)
Kaixuan Zeng (5802707)
Xiangxiang Liu (617225)
Xueni Xu (5802710)
Bei Pan (5560136)
Tao Xu (3537)
Li Sun (4624)
Bangshun He (119526)
Yuqin Pan (119528)
Huiling Sun (530956)
Shukui Wang (119550)

January 2019

Table S1. The list of primers and probes. Table S2. SiRNAs and sh-RNAs sequence. Table S3. Informati...

Additional file 4: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Feng Liang (447805)
Hongzhu Qu (36515)
Qiang Lin (208776)
Yadong Yang (396824)
Xiuyan Ruan (3450233)
Bo Zhang (6559)
Yi Liu (36759)
Chengze Yu (3450230)
Hongyan Zhang (618068)
Xiangdong Fang (180671)
Xiaopeng Hao (1644652)

August 2015

Classification of genes based on the expression levels. A table showing how the gene expression leve...

Additional file 7: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Feng Liang (447805)
Hongzhu Qu (36515)
Qiang Lin (208776)
Yadong Yang (396824)
Xiuyan Ruan (3450233)
Bo Zhang (6559)
Yi Liu (36759)
Chengze Yu (3450230)
Hongyan Zhang (618068)
Xiangdong Fang (180671)
Xiaopeng Hao (1644652)

August 2015

A KEGG pathway figure for the enriched pathway B cell receptor signaling pathway in down-regulated g...

Additional file 3: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Feng Liang (447805)
Hongzhu Qu (36515)
Qiang Lin (208776)
Yadong Yang (396824)
Xiuyan Ruan (3450233)
Bo Zhang (6559)
Yi Liu (36759)
Chengze Yu (3450230)
Hongyan Zhang (618068)
Xiangdong Fang (180671)
Xiaopeng Hao (1644652)

August 2015

Scatter plots of gene expression values between samples. A figure illustrating how similar of genes ...

Additional file 8: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Feng Liang (447805)
Hongzhu Qu (36515)
Qiang Lin (208776)
Yadong Yang (396824)
Xiuyan Ruan (3450233)
Bo Zhang (6559)
Yi Liu (36759)
Chengze Yu (3450230)
Hongyan Zhang (618068)
Xiangdong Fang (180671)
Xiaopeng Hao (1644652)

August 2015

The schematic diagram of other fused genes. A figure showing how the rest of gene fusions occurred. ...

Additional file 2: of Molecular patterns of cancer colonisation in lymph nodes of breast cancer patients

Gaurav Chatterjee (5998253)
Trupti Pai (5998256)
Thomas Hardiman (5876474)
Kelly Avery-Kiejda (3534812)
Rodney Scott (279337)
Jo Spencer (267903)
Sarah Pinder (553692)
Anita Grigoriadis (41195)

November 2018

Table S2. Genes found to be differentially expressed in multiple studies included in scenario 1 (inv...

Additional file 7: of Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma

Akanksha Verma (3553664)
Yanwen Jiang (103833)
Wei Du (88790)
Lauren Fairchild (3553661)
Ari Melnick (88754)
Olivier Elemento (7617)

November 2015

List of protein-coding genes correlated with lncRNAs. Each protein-coding gene co-expressed with a n...

Additional file 1: of RNA-sequencing in non-small cell lung cancer shows gene downregulation of therapeutic targets in tumor tissue compared to non-malignant lung tissue

Kobe Reynders (5526461)
Els Wauters (101718)
Matthieu Moisse (659185)
Herbert DecaluwĂŠ (5526488)
Paul De Leyn (5526455)
StĂŠphanie Peeters (5526485)
Maarten Lambrecht (5526458)
Kristiaan Nackaerts (3210705)
Christophe Dooms (2938749)
Wim Janssens (101722)
Johan Vansteenkiste (5526467)
Diether Lambrechts (101772)
Dirk De Ruysscher (810406)

July 2018

Table S1. RNA-sequencing results for tumor tissue (a) or non-malignant lung tissue (b). Differential...

Additional file 5: of Molecular patterns of cancer colonisation in lymph nodes of breast cancer patients

Gaurav Chatterjee (5998253)
Trupti Pai (5998256)
Thomas Hardiman (5876474)
Kelly Avery-Kiejda (3534812)
Rodney Scott (279337)
Jo Spencer (267903)
Sarah Pinder (553692)
Anita Grigoriadis (41195)

November 2018

Table S5. Differentially expressed genes representing specific immune cell populations across all th...

Additional file 6: of PLAIDOH: a novel method for functional prediction of long non-coding RNAs identifies cancer-specific LncRNA activities

Sarah Pyfrom (6370442)
Hong Luo (205745)
Jacqueline Payton (6370448)

February 2019

Figure S5. LncRNAs demonstrate common or cancer-type specific positive or negative correlation profi...

Additional file 6: of Mutation status coupled with RNA-sequencing data can efficiently identify important non-significantly mutated genes serving as diagnostic biomarkers of endometrial cancer

Keqin Liu (4725318)
Li He (134049)
Zhichao Liu (191718)
Junmei Xu (4725315)
Yuan Liu (88411)
Qifan Kuang (624438)
Zhining Wen (226349)
Menglong Li (226358)

December 2017

Summary of 1273 non-SMGs showed different expression patterns in the groups of histological type pat...

Additional file 3: Table S2. of Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

M. Ampuja (3631321)
T. Rantapero (3631318)
A. Rodriguez-Martinez (3631312)
M. Palmroth (3631327)
E. Alarmo (3631309)
M. Nykter (3631315)
A. Kallioniemi (3631324)

January 2017

Differentially expressed genes after BMP4 treatment in T-47D cell line. Ensembl IDs, read counts, fo...

Additional file 1: of Molecular patterns of cancer colonisation in lymph nodes of breast cancer patients

Gaurav Chatterjee (5998253)
Trupti Pai (5998256)
Thomas Hardiman (5876474)
Kelly Avery-Kiejda (3534812)
Rodney Scott (279337)
Jo Spencer (267903)
Sarah Pinder (553692)
Anita Grigoriadis (41195)

November 2018

Table S1. Gene list compiled from all the studies included in scenario 1 (involved LN versus primary...

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 4 of A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping

Qing Wen (808516)
Chang-Sik Kim (3045420)
Peter Hamilton (438342)
Shu-Dong Zhang (231229)

May 2016

Breast cancer gene signature. The full list of 232 genes (probesets) and their ranks for the optimal...

Additional file 1: of lncRNA SNHG6 regulates EZH2 expression by sponging miR-26a/b and miR-214 in colorectal cancer

Mu Xu (594466)
Xiaoxiang Chen (730749)
Kang Lin (5530313)
Kaixuan Zeng (5802707)
Xiangxiang Liu (617225)
Xueni Xu (5802710)
Bei Pan (5560136)
Tao Xu (3537)
Li Sun (4624)
Bangshun He (119526)
Yuqin Pan (119528)
Huiling Sun (530956)
Shukui Wang (119550)

January 2019

Table S1. The list of primers and probes. Table S2. SiRNAs and sh-RNAs sequence. Table S3. Informati...

Additional file 6: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Abstract

Extracted data

Additional file 6: of Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes

Abstract

Extracted data

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