Global Gene Coexpression Search tool MEM

by Anna Ufliand

Bioinformatics Seminar, 30.09.2016

Gene Expression

Central Dogma of Molecular Biology

Image: Your Genome

http://dharmacon.gelifesciences.com/applications/gene-expression/

Gene Expression

http://dharmacon.gelifesciences.com/applications/gene-expression/

Gene Expression

Sample

Biological magic

https://en.wikipedia.org/wiki/DNA_microarray

Measuring Gene Expression

Sample

Biological magic

Sample

Biological magic

Sample

Biological magic

Sample

Biological magic

Sample

Biological magic

Experiment

http://advan.physiology.org

Control Test

Sample 1

Sample 2

Sample 3

Sample 4

Sample 5 … Sample

Gene 1 45 36 96 23 20 40

Gene 2 10 27 54 50 43 27

Gene 3 13 11 99 61 49 73

Gene 4 61 29 12 0 21 44

Gene 5 8 0 41 72 14 93

Gene 6 0 5 23 7 48 13

… 85

Gene M 12 36 9 81 38 40

DatasetControl TestTestTest Control Control

Sample 1

Sample 2

Sample 3

Sample 4

Sample 5 … Sample

Gene 1 0.1967 -1.8514 -0.0115 -0.0809 0.8563 0.8910

Gene 2 -0.7564 1.1564 -0.5080 -0.6347 1.1011 -0.2130

Gene 3 -1.9670 -1.2569 0.4944 1.2508 0.4379 -0.5839

Gene 4 0.4397 -0.4066 -0.5809 -0.2741 -1.5064 2.2165

Gene 5 0.2872 -2.7630 -0.0171 -0.1221 1.2823 1.3415

Gene 6 -1.3435 0.8683 -2.1044 -0.5460 -0.0450 -1.6893

Gene M 0.3125 0.1237 1.6664 -0.9484 0.3885 2.0640

Normalised dataset

Normalised datasetSample

1Sample

2Sample

3Sample

4Sample

5 … Sample N

Gene 1 0.1967 -1.8514 -0.0115 -0.0809 0.8563 0.8910

Gene 2 -0.7564 1.1564 -0.5080 -0.6347 1.1011 -0.2130

Gene 3 -1.9670 -1.2569 0.4944 1.2508 0.4379 -0.5839

Gene 4 0.4397 -0.4066 -0.5809 -0.2741 -1.5064 2.2165

Gene 5 0.2872 -2.7630 -0.0171 -0.1221 1.2823 1.3415

Gene 6 -1.3435 0.8683 -2.1044 -0.5460 -0.0450 -1.6893

Gene M 0.3125 0.1237 1.6664 -0.9484 0.3885 2.0640

Coexpressed genesco

Sample 1

Sample 2

Sample 3

Sample 4

Sample 5 … Sample

Gene 1 0.1967 -1.8514 -0.0115 -0.0809 0.8563 0.8910

Gene 5 0.2872 -2.7630 -0.0171 -0.1221 1.2823 1.3415

Gene 1

Gene 5

Biological meaning

Gene 1

Gene 5

Biological meaning

Gene 1

Gene 5

Biological meaning

Gene 1

Gene 5

Biological meaning

Sample 1

Sample 2

Sample 3

Sample 4

Sample 5 … Sample

Gene 1 0.1967 -1.8514 -0.0115 -0.0809 0.8563 0.8910

Gene 2 -0.7564 1.1564 -0.5080 -0.6347 1.1011 -0.2130

Gene 3 -1.9670 -1.2569 0.4944 1.2508 0.4379 -0.5839

Gene 4 0.4397 -0.4066 -0.5809 -0.2741 -1.5064 2.2165

Gene 5 0.2872 -2.7630 -0.0171 -0.1221 1.2823 1.3415

Gene 6 -1.3435 0.8683 -2.1044 -0.5460 -0.0450 -1.6893

Gene M 0.3125 0.1237 1.6664 -0.9484 0.3885 2.0640

We have a dataset

Sample 1

Sample 2

Sample 3

Sample 4

Sample 5 … Sample

Gene 1 0.1967 -1.8514 -0.0115 -0.0809 0.8563 0.8910

Gene 2 -0.7564 1.1564 -0.5080 -0.6347 1.1011 -0.2130

Gene 3 -1.9670 -1.2569 0.4944 1.2508 0.4379 -0.5839

Gene 4 0.4397 -0.4066 -0.5809 -0.2741 -1.5064 2.2165

Gene 5 0.2872 -2.7630 -0.0171 -0.1221 1.2823 1.3415

Gene 6 -1.3435 0.8683 -2.1044 -0.5460 -0.0450 -1.6893

Gene M 0.3125 0.1237 1.6664 -0.9484 0.3885 2.0640

Select query gene

Sample 1

Sample 2

Sample 3

Sample 4

Sample 5 … Sample

Gene 1 0.1967 -1.8514 -0.0115 -0.0809 0.8563 0.8910

Gene 5 0.2872 -2.7630 -0.0171 -0.1221 1.2823 1.3415

Gene 6 -1.3435 0.8683 -2.1044 -0.5460 -0.0450 -1.6893

Gene 4 0.4397 -0.4066 -0.5809 -0.2741 -1.5064 2.2165

Gene 3 -1.9670 -1.2569 0.4944 1.2508 0.4379 -0.5839

Gene 2 -0.7564 1.1564 -0.5080 -0.6347 1.1011 -0.2130

Gene M 0.3125 0.1237 1.6664 -0.9484 0.3885 2.0640

Order by coexpression

1 2 3 4 5 … N11 0.4

15.3 0.8

1-2.3 1.9 5.1

2 10.6

27 54 50 42 203 0.1

311 2 87 41 81

4 1.61

52 13 4 18 395 -0.7 0 41 69 14 936 1.1 4 12 6 48 13… 85M1 -0.9 25 98 81 38 40

1 2 3 4 5 … N21 4.1 0.3

69.3 -0.2

32.3 -4.1

2 -2.7 27 54 50 43 273 7.3 11 99 61 49 734 -1.1 29 12 0 21 445 0.7 0 41 72 14 936 -1.1 5 23 7 48 13… 85M2 2.4 36 9 81 38 40

1 2 3 4 5 … N31 4.5 3.6 0.9

6-2.3 2.1

2 -0.1 27 54 50 43 273 1.3 11 99 61 49 734 0.6

129 12 0 21 44

5 -0.8 0 41 72 14 936 0.1 5 23 7 48 13… 85M3 -1.2 36 9 81 38 40

1 2 3 4 5 … N41 0.6 3.6 96 23 20 402 0.1 -2.7 39 50 43 273 -1.1 1.1 99 61 49 734 0.5 4.8 12 0 18 445 -0.8 -2.1

141 72 14 93

6 0.1 1.1 23 7 48 13… 85M4 0.8 0.3 9 81 38 40

1 2 3 4 5 … Nk1 4.5 0.6 0.96 -2.3 20 0.42 -0.1 2.4 543 5.1 43 2.73 1.3 -1.3 1.9 -0.6

149 -7.3

4 -1.1 2.9 0.12 0.12 21 0.445 0.8 0.1 -4.1 0.72 14 0.936 -2.1 -2.7 -0.2

3-0.3 48 1.3

…Mk 1.2 3.6 1.9 8.1 -3.8 -0.4

http://www.ebi.ac.uk/arrayexpress/browse.html

1 2 3 4 5 … N11 0.4

15.3 0.8

1-2.3 1.9 5.1

2 10.6

27 54 50 42 203 0.1

311 2 87 41 81

4 1.61

52 13 4 18 395 -0.7 0 41 69 14 936 1.1 4 12 6 48 13… 85M1 -0.9 25 98 81 38 40

1 2 3 4 5 … N21 4.1 0.3

69.3 -0.2

32.3 -4.1

2 -2.7 27 54 50 43 273 7.3 11 99 61 49 734 -1.1 29 12 0 21 445 0.7 0 41 72 14 936 -1.1 5 23 7 48 13… 85M2 2.4 36 9 81 38 40

1 2 3 4 5 … N31 4.5 3.6 0.9

6-2.3 2.1

2 -0.1 27 54 50 43 273 1.3 11 99 61 49 734 0.6

129 12 0 21 44

5 -0.8 0 41 72 14 936 0.1 5 23 7 48 13… 85M3 -1.2 36 9 81 38 40

1 2 3 4 5 … N41 0.6 3.6 96 23 20 402 0.1 -2.7 39 50 43 273 -1.1 1.1 99 61 49 734 0.5 4.8 12 0 18 445 -0.8 -2.1

141 72 14 93

6 0.1 1.1 23 7 48 13… 85M4 0.8 0.3 9 81 38 40

1 2 3 4 5 … Nk1 4.5 0.6 0.96 -2.3 20 0.42 -0.1 2.4 543 5.1 43 2.73 1.3 -1.3 1.9 -0.6

149 -7.3

4 -1.1 2.9 0.12 0.12 21 0.445 0.8 0.1 -4.1 0.72 14 0.936 -2.1 -2.7 -0.2

3-0.3 48 1.3

…Mk 1.2 3.6 1.9 8.1 -3.8 -0.4

Global coexpression

Measuring global coexpression

RRA (Robust Rank Aggregation)

http://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-12-r139

gene rank

3 1016

… …

gene rank

2 1425

5 1250

… …

gene rank

3 1013

4 1271

5 1687

… …

gene rank

2 1026

4 1356

… …

Query gene: NANOGds 1 ds 2 ds 3 ds K

gene rank

3 1016

… …

gene rank

2 1425

5 1250

… …

gene rank

1 1076

3 1013

4 1271

5 1687

… …

gene rank

2 1026

4 1356

… …

gene rank

3 1016

… …

gene rank

2 1425

… …

gene rank

1 1076

3 1013

4 1271

… …

gene rank

2 1026

4 1356

… …

Null hypothesis: uniform distribution of ranks

Significant coexpression: distribution is skewed to lower ranks

1 2 3 4 5 … N11 0.4

15.3 0.8

1-2.3 1.9 5.1

2 10.6

27 54 50 42 203 0.1

311 2 87 41 81

4 1.61

52 13 4 18 395 -0.7 0 41 69 14 936 1.1 4 12 6 48 13… 85M1 -0.9 25 98 81 38 40

1 2 3 4 5 … N21 4.1 0.3

69.3 -0.2

32.3 -4.1

2 -2.7 27 54 50 43 273 7.3 11 99 61 49 734 -1.1 29 12 0 21 445 0.7 0 41 72 14 936 -1.1 5 23 7 48 13… 85M2 2.4 36 9 81 38 40

1 2 3 4 5 … N31 4.5 3.6 0.9

6-2.3 2.1

2 -0.1 27 54 50 43 273 1.3 11 99 61 49 734 0.6

129 12 0 21 44

5 -0.8 0 41 72 14 936 0.1 5 23 7 48 13… 85M3 -1.2 36 9 81 38 40

1 2 3 4 5 … N41 0.6 3.6 96 23 20 402 0.1 -2.7 39 50 43 273 -1.1 1.1 99 61 49 734 0.5 4.8 12 0 18 445 -0.8 -2.1

141 72 14 93

6 0.1 1.1 23 7 48 13… 85M4 0.8 0.3 9 81 38 40

1 2 3 4 5 … Nk1 4.5 0.6 0.96 -2.3 20 0.42 -0.1 2.4 543 5.1 43 2.73 1.3 -1.3 1.9 -0.6

149 -7.3

4 -1.1 2.9 0.12 0.12 21 0.445 0.8 0.1 -4.1 0.72 14 0.936 -2.1 -2.7 -0.2

3-0.3 48 1.3

…Mk 1.2 3.6 1.9 8.1 -3.8 -0.4

Global coexpression

MEM tool (Multi Experiment Matrix)

http://biit.cs.ut.ee/beta_mem/

What we learnt today:

• What is gene expression and how to measure it

• What is coexpression and how to measure it

• What is Global coexpression and how to measure it

• What is MEM and how to use it

What did we learn today:

Global Gene Coexpression Search tool MEM

Documents

coexpression modules robust to sample collection and ... · 1 1 Meta-analysis of the human brain transcriptome identifies heterogeneity across human AD 2 coexpression modules robust

karunadu.karnataka.gov.in › ldakarnataka › Documents › Mem… · FUNCTIONS OF THE Restoring i@kes and facilitation oresto:-aåcn table. Diver±ã / trea±g sewaca- tc gene-rate

COXPRESdb gene coexpression database for Human, …pdbj.org/workshop/20090729/IUPS2009_COXPRESdb_Introduction.pdf · gene coexpression database for Human, mouse and rat ... 2006:

Identifying gene coexpression networks underlying the

Original Article · 2016. 1. 31. · Chemoarchitecture Chemoarchitecture reports as collated from the literature Coexpression Reports of molecule coexpression identified in different

savur.meb.gov.tr · Web viewMardin MEM İSGB. Mardin MEM İSGB. Mardin MEM İSGB. Mardin MEM İSGB. Mardin MEM İSGBBaşa Dön. Mardin MEM İSGB. Başa Dön. Mardin MEM İSGB. Mardin

Comparative Analysis of Gene-Coexpression Networks Across Species

Comparative transcriptomics method to infer gene ...Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes

Running head: Coexpression Networks of Phosphate ... · 1/19/2011 · coexpression gene clusters using a PC. In addition, this utility allows deducing organ- and tissue-specific

Coexpression of a Multidrug-resistance Gene (MDR1) and ... · Simplex Virus Thymidine Kinase Gene as Part of a Bicistronic Messenger RNA in a Retrovirus Vector Allows Selective Killing

Gene coexpression measures in large ... - ict.ac.cnbioinfo.ict.ac.cn/~dbu/AlgorithmCourses/Lectures... · Gene coexpression measures in large heterogeneous samples using count statistics

Gene Expression Platforms for Global Coexpression Analyses Assessment and Integration for Study of Gene Deregulation in Cancer Obi Griffith, Erin Pleasance,

Research Article Characterization of Genes for Beef Marbling … · 2019. 7. 31. · Research Article Characterization of Genes for Beef Marbling Based on Applying Gene Coexpression

A Developmental Transcriptional Network for Maize Deines Coexpression Modules1[C]

MYC/BCL2 protein coexpression contributes inferior outcome in DLBCL

Unbiased transcriptomic analyses reveal distinct effects ... · WT mice after SCI. Weighted gene-coexpression net-work analysis (WGCNA) of spinal cord transcriptomes revealed that

Unique coexpression in osteoblasts of broadly expressed

COXPRESdb gene coexpression database for Human, mouse and …

Differential Weighted Gene Coexpression Network Analysis Applied to Mouse Weight Tova Fuller Steve Horvath Department of Human Genetics University of California,

Gene Coexpression Network Alignment and Conservation of ... · Plant and Environmental Sciences (S.P.F., F.A.F.) and Department of Genetics and Biochemistry (F.A.F.), Clemson University,