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Gene enrichment analysis—Highlights from gene ontology, KEGG pathways, reactome pathways.

Kristopher J. L. Irizarry (4395175)
Eileen Downs (4395190)
Randall Bryden (4395184)
Jory Clark (4395202)
Lisa Griggs (4395196)
Renee Kopulos (4395205)
Cynthia M. Boettger (4395193)
Thomas J. Carr Jr. (4395187)
Calvin L. Keeler (4395181)
Ellen Collisson (4395178)
Yvonne Drechsler (4395199)

Publication date

August 2017

DOI

10.1371/journal.pone.0179391.t003

Abstract

<p>Gene enrichment analysis—Highlights from gene ontology, KEGG pathways, reactome pathways.</p

Extracted data

Related items

The KEGG enrichment analysis showing that the differentially expressed genes are significantly involved in the predicted pathways.

Jianqin Zhang (549793)
Fuzhu Liu (748212)
Junting Cao (748213)
Xiaolin Liu (403100)

June 2015

<p>Note: S gene represents the number of significant genes that were expressed; TS gene represents t...

Molecular enrichment associations – GO: Molecular Functions and KEGG pathways.

Bhairavi Swaminathan (406575)
Haize Goikuria (673868)
Reyes Vega (673869)
Alfredo Rodríguez-Antigüedad (673870)
Antonio López Medina (673871)
María del Mar Freijo (673872)
Koen Vandenbroeck (335818)
Iraide Alloza (406577)

December 2014

<p>Molecular enrichment associations – GO: Molecular Functions and KEGG pathways.</p

Gene enrichemnt analysis for KEGG Pathway terms using Metascape

Sora Yonezawa (14618045)

August 2023

Using the "Custum Analysis" feature of Metascape (accessed; 23/08/15) , an enrichment analysis was ...

Pathways enrichment analysis within up and downregulated genes using KEGG and Metacore databases.

Sarah Uboldi (170857)
Enrica Calura (170860)
Luca Beltrame (67207)
Ilaria Fuso Nerini (170861)
Sergio Marchini (170863)
Duccio Cavalieri (148329)
Eugenio Erba (170865)
Giovanna Chiorino (64687)
Paola Ostano (141378)
Daniela D'Angelo (170867)
Maurizio D'Incalci (170869)
Chiara Romualdi (10215)

April 2012

<p>Pathways enrichment analysis within up and downregulated genes using KEGG and Metacore databases....

Gene Ontology categories and KEGG, PANTHER and Metacore pathway enrichment analysis within up and down regulated proteins.

Sarah Uboldi (170857)
Enrica Calura (170860)
Luca Beltrame (67207)
Ilaria Fuso Nerini (170861)
Sergio Marchini (170863)
Duccio Cavalieri (148329)
Eugenio Erba (170865)
Giovanna Chiorino (64687)
Paola Ostano (141378)
Daniela D'Angelo (170867)
Maurizio D'Incalci (170869)
Chiara Romualdi (10215)

April 2012

<p>Gene Ontology categories and KEGG, PANTHER and Metacore pathway enrichment analysis within up and...

KEGG analysis of enriched pathways of differentially expressed genes between two groups.

Bao Yi (495702)
Liang Chen (73736)
Renna Sa (728624)
Ruqing Zhong (3112197)
Huan Xing (3112200)
Hongfu Zhang (230929)

September 2016

<p>KEGG analysis of enriched pathways of differentially expressed genes between two groups.</p

Significant enrichment analysis of differentially expressed genes in top 20 KEGG pathways.

Daizhen Zhang (5728403)
Jun Liu (42548)
Tingting Qi (710630)
Baoming Ge (5728406)
Qiuning Liu (5728409)
Senhao Jiang (5728412)
Huabin Zhang (798548)
Zhengfei Wang (303878)
Ge Ding (5728415)
Boping Tang (322718)

September 2018

Significant enrichment analysis of differentially expressed genes in top 20 KEGG pathways.</p

Pathway enrichment analysis of differentially expressed genes (Top ten enriched pathways are shown).

Jingjuan Li (795743)
Qian Ding (686082)
Fengde Wang (5665297)
Yihui Zhang (578676)
Huayin Li (795744)
Jianwei Gao (795745)

September 2015

<p>Pathway enrichment analysis of differentially expressed genes (Top ten enriched pathways are show...

Gene enrichment results carried out using the Gene Ontology (GO) enrichment analysis web-based bioinformatics tool WEB-based GEne SeT AnaLysis Toolkit (WebGestalt).

Alessandra Allione (749744)
Francesca Marcon (749745)
Giovanni Fiorito (136942)
Simonetta Guarrera (136940)
Ester Siniscalchi (749746)
Andrea Zijno (375688)
Riccardo Crebelli (749747)
Giuseppe Matullo (136983)

June 2015

<p>Gene enrichment results carried out using the Gene Ontology (GO) enrichment analysis web-based bi...

List of pathways obtained by KEGG pathway enrichment analysis of some of these identified proteins.

Varun Chhabra (5513573)
Avnika Singh Anand (5513564)
Amit Kumar Baidya (5513567)
Shajer Manzoor Malik (5513576)
Ekta Kohli (92380)
Maramreddy Prasanna Kumar Reddy (5513570)

July 2018

<p>List of pathways obtained by KEGG pathway enrichment analysis of some of these identified protein...

KEGG pathway enrichment analysis of differentially expressed genes between S28 and S6.

Tangjian Peng (4037189)
Liyuan Ma (534132)
Xue Feng (147580)
Jiemeng Tao (4037192)
Meihua Nan (4037186)
Yuandong Liu (2416462)
Jiaokun Li (4037195)
Li Shen (110858)
Xueling Wu (53374)
Runlan Yu (4037183)
Xueduan Liu (519039)
Guanzhou Qiu (579966)
Weimin Zeng (4037180)

May 2017

<p>Enrichment factor is calculated as followed: </p><p></p> Gene hits is the number of hits in the s...

Enrichment analysis on six Gene Ontology terms (biological processes).

Woochang Hwang (87586)
Laszlo Hackler Jr. (129803)
George Wu (129805)
Hongkai Ji (22411)
Donald J. Zack (9715)
Jiang Qian (771)

October 2012

<p>Enrichment analysis for the genes specifically expressed in six development time points. X-axis i...

KEGG pathway enrichment analysis of differentially expressed genes between TTCS and TTE75.

Bo Liu (127343)
Yuhong Zhang (268338)
Wei Zhang (405)

March 2014

<p>KEGG pathway enrichment analysis of differentially expressed genes between TTCS and TTE75.</p

Gene set enrichment of cell type-specific gene lists – MsigDB C2 KEGG Canonical Pathways

Casey P. Shannon (532280)
Robert Balshaw (399184)
Raymond T. Ng (253624)
Janet E. Wilson-McManus (532281)
Paul Keown (551708)
Robert McMaster (551709)
Bruce M. McManus (351410)
David Landsberg (551710)
Nicole M. Isbel (551711)
Greg Knoll (163065)
Scott J. Tebbutt (219490)

April 2014

<p>Gene set enrichment of cell type-specific gene lists – MsigDB C2 KEGG Canonical Pathways</p

Enrichment analysis of KEGG pathways in comparisons of different stages.

Cong-Hui Yang (3080421)
Peng-Cheng Yang (3080424)
Jing Li (10611)
Fan Yang (1413)
Ai-Bing Zhang (112425)

August 2016

<p>The x-axis indicates the p value calculated in enrichment test. The size of circles indicates the...

The KEGG enrichment analysis showing that the differentially expressed genes are significantly involved in the predicted pathways.

Jianqin Zhang (549793)
Fuzhu Liu (748212)
Junting Cao (748213)
Xiaolin Liu (403100)

June 2015

<p>Note: S gene represents the number of significant genes that were expressed; TS gene represents t...

Molecular enrichment associations – GO: Molecular Functions and KEGG pathways.

Bhairavi Swaminathan (406575)
Haize Goikuria (673868)
Reyes Vega (673869)
Alfredo Rodríguez-Antigüedad (673870)
Antonio López Medina (673871)
María del Mar Freijo (673872)
Koen Vandenbroeck (335818)
Iraide Alloza (406577)

December 2014

<p>Molecular enrichment associations – GO: Molecular Functions and KEGG pathways.</p

Gene enrichemnt analysis for KEGG Pathway terms using Metascape

Sora Yonezawa (14618045)

August 2023

Using the "Custum Analysis" feature of Metascape (accessed; 23/08/15) , an enrichment analysis was ...

Pathways enrichment analysis within up and downregulated genes using KEGG and Metacore databases.

Sarah Uboldi (170857)
Enrica Calura (170860)
Luca Beltrame (67207)
Ilaria Fuso Nerini (170861)
Sergio Marchini (170863)
Duccio Cavalieri (148329)
Eugenio Erba (170865)
Giovanna Chiorino (64687)
Paola Ostano (141378)
Daniela D'Angelo (170867)
Maurizio D'Incalci (170869)
Chiara Romualdi (10215)

April 2012

<p>Pathways enrichment analysis within up and downregulated genes using KEGG and Metacore databases....

Gene Ontology categories and KEGG, PANTHER and Metacore pathway enrichment analysis within up and down regulated proteins.

Sarah Uboldi (170857)
Enrica Calura (170860)
Luca Beltrame (67207)
Ilaria Fuso Nerini (170861)
Sergio Marchini (170863)
Duccio Cavalieri (148329)
Eugenio Erba (170865)
Giovanna Chiorino (64687)
Paola Ostano (141378)
Daniela D'Angelo (170867)
Maurizio D'Incalci (170869)
Chiara Romualdi (10215)

April 2012

<p>Gene Ontology categories and KEGG, PANTHER and Metacore pathway enrichment analysis within up and...

KEGG analysis of enriched pathways of differentially expressed genes between two groups.

Bao Yi (495702)
Liang Chen (73736)
Renna Sa (728624)
Ruqing Zhong (3112197)
Huan Xing (3112200)
Hongfu Zhang (230929)

September 2016

<p>KEGG analysis of enriched pathways of differentially expressed genes between two groups.</p

Significant enrichment analysis of differentially expressed genes in top 20 KEGG pathways.

Daizhen Zhang (5728403)
Jun Liu (42548)
Tingting Qi (710630)
Baoming Ge (5728406)
Qiuning Liu (5728409)
Senhao Jiang (5728412)
Huabin Zhang (798548)
Zhengfei Wang (303878)
Ge Ding (5728415)
Boping Tang (322718)

September 2018

Significant enrichment analysis of differentially expressed genes in top 20 KEGG pathways.</p

Pathway enrichment analysis of differentially expressed genes (Top ten enriched pathways are shown).

Jingjuan Li (795743)
Qian Ding (686082)
Fengde Wang (5665297)
Yihui Zhang (578676)
Huayin Li (795744)
Jianwei Gao (795745)

September 2015

<p>Pathway enrichment analysis of differentially expressed genes (Top ten enriched pathways are show...

Gene enrichment results carried out using the Gene Ontology (GO) enrichment analysis web-based bioinformatics tool WEB-based GEne SeT AnaLysis Toolkit (WebGestalt).

Alessandra Allione (749744)
Francesca Marcon (749745)
Giovanni Fiorito (136942)
Simonetta Guarrera (136940)
Ester Siniscalchi (749746)
Andrea Zijno (375688)
Riccardo Crebelli (749747)
Giuseppe Matullo (136983)

June 2015

<p>Gene enrichment results carried out using the Gene Ontology (GO) enrichment analysis web-based bi...

List of pathways obtained by KEGG pathway enrichment analysis of some of these identified proteins.

Varun Chhabra (5513573)
Avnika Singh Anand (5513564)
Amit Kumar Baidya (5513567)
Shajer Manzoor Malik (5513576)
Ekta Kohli (92380)
Maramreddy Prasanna Kumar Reddy (5513570)

July 2018

<p>List of pathways obtained by KEGG pathway enrichment analysis of some of these identified protein...

KEGG pathway enrichment analysis of differentially expressed genes between S28 and S6.

Tangjian Peng (4037189)
Liyuan Ma (534132)
Xue Feng (147580)
Jiemeng Tao (4037192)
Meihua Nan (4037186)
Yuandong Liu (2416462)
Jiaokun Li (4037195)
Li Shen (110858)
Xueling Wu (53374)
Runlan Yu (4037183)
Xueduan Liu (519039)
Guanzhou Qiu (579966)
Weimin Zeng (4037180)

May 2017

<p>Enrichment factor is calculated as followed: </p><p></p> Gene hits is the number of hits in the s...

Enrichment analysis on six Gene Ontology terms (biological processes).

Woochang Hwang (87586)
Laszlo Hackler Jr. (129803)
George Wu (129805)
Hongkai Ji (22411)
Donald J. Zack (9715)
Jiang Qian (771)

October 2012

<p>Enrichment analysis for the genes specifically expressed in six development time points. X-axis i...

KEGG pathway enrichment analysis of differentially expressed genes between TTCS and TTE75.

Bo Liu (127343)
Yuhong Zhang (268338)
Wei Zhang (405)

March 2014

<p>KEGG pathway enrichment analysis of differentially expressed genes between TTCS and TTE75.</p

Gene set enrichment of cell type-specific gene lists – MsigDB C2 KEGG Canonical Pathways

Casey P. Shannon (532280)
Robert Balshaw (399184)
Raymond T. Ng (253624)
Janet E. Wilson-McManus (532281)
Paul Keown (551708)
Robert McMaster (551709)
Bruce M. McManus (351410)
David Landsberg (551710)
Nicole M. Isbel (551711)
Greg Knoll (163065)
Scott J. Tebbutt (219490)

April 2014

<p>Gene set enrichment of cell type-specific gene lists – MsigDB C2 KEGG Canonical Pathways</p

Enrichment analysis of KEGG pathways in comparisons of different stages.

Cong-Hui Yang (3080421)
Peng-Cheng Yang (3080424)
Jing Li (10611)
Fan Yang (1413)
Ai-Bing Zhang (112425)

August 2016

<p>The x-axis indicates the p value calculated in enrichment test. The size of circles indicates the...

The KEGG enrichment analysis showing that the differentially expressed genes are significantly involved in the predicted pathways.

Jianqin Zhang (549793)
Fuzhu Liu (748212)
Junting Cao (748213)
Xiaolin Liu (403100)

June 2015

<p>Note: S gene represents the number of significant genes that were expressed; TS gene represents t...

Molecular enrichment associations – GO: Molecular Functions and KEGG pathways.

Bhairavi Swaminathan (406575)
Haize Goikuria (673868)
Reyes Vega (673869)
Alfredo Rodríguez-Antigüedad (673870)
Antonio López Medina (673871)
María del Mar Freijo (673872)
Koen Vandenbroeck (335818)
Iraide Alloza (406577)

December 2014

<p>Molecular enrichment associations – GO: Molecular Functions and KEGG pathways.</p

Gene enrichemnt analysis for KEGG Pathway terms using Metascape

Sora Yonezawa (14618045)

August 2023

Using the "Custum Analysis" feature of Metascape (accessed; 23/08/15) , an enrichment analysis was ...