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Protocols

MEM specifications

Information


Unique identifier OMICS_03441
Name MEM
Alternative name Multi Experiment Matrix
Interface Web user interface
Restrictions to use None
Input data A single query gene.
Output data A ranked list of genes that are coexpressed with the query gene in the provided datasets.
Biological technology Affymetrix
Programming languages C++, Javascript, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Documentation


Maintainers


  • person_outline Jaak Vilo
  • person_outline Raivo Kolde
  • person_outline Priit Adler

Additional information


https://biit.cs.ut.ee/mem/help/help.html

Publication for Multi Experiment Matrix

MEM citations

 (16)
library_books

Long non coding RNAs RP5 821D11.7, APCDD1L AS1 and RP11 277P12.9 were associated with the prognosis of lung squamous cell carcinoma

2018
PMCID: 5928681
PMID: 29568882
DOI: 10.3892/mmr.2018.8770

[…] Associated genes (co-expression genes) of lncRNAs were obtained through the Human RNAseq expression data platform in the Multi-Experiment Matrix (MEM; biit.cs.ut.ee/mem/index.cgi) online tool (). Using the STRING database (string-db.org) (), a protein-protein interaction (PPI) network was established, with an associated […]

library_books

Bioinformatics analysis of differentially expressed gene profiles associated with systemic lupus erythematosus

2017
PMCID: 5802164
PMID: 29257335
DOI: 10.3892/mmr.2017.8293

[…] e Molecular Complex Detection (MCODE) algorithm is an established automated method to find highly interconnected modules as molecular complexes or clusters in large PPI networks (). Additionally, the Multi Experiment Matrix (MEM; biit.cs.ut.ee/mem/index.cgi) () is a web-based multi experiment gene expression query and visualization tool. It gathers hundreds of publicly available gene expression da […]

library_books

Gene expression signatures of neuroendocrine prostate cancer and primary small cell prostatic carcinoma

2017
BMC Cancer
PMCID: 5683385
PMID: 29132337
DOI: 10.1186/s12885-017-3729-z

[…] ese genes were highly correlated in meta-analysis datasets (r=0.70-0.93). PHYHIPL probe-set 226623_at moreover had the top co-expression similarity score (3.2e-138) to CCEPR probe-set 228679_at under Multi-Experiment Matrix analysis based on hundreds of Affymetrix datasets [].Meta-12 genes were derived from conceptually similar criteria underlying the recent integrated NEPC classifier []. We adopt […]

library_books

Long non coding RNA HOTTIP promotes hepatocellular carcinoma tumorigenesis and development: A comprehensive investigation based on bioinformatics, qRT PCR and meta analysis of 393 cases

2017
PMCID: 5673011
PMID: 29039502
DOI: 10.3892/ijo.2017.4164

[…] CC remain elusive ().In the present study, we investigated the expression of HOTTIP in HCC and normal liver. Furthermore, we combined Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), Multi Experiment Matrix (MEM) and Oncomine database, quantitative reverse transcription-polymerase chain reactions (qRT-PCR), and meta-analysis to assess the clinical role and the potential molecular […]

library_books

Long non coding RNA polymorphisms in 6p21.1 are associated with atrophic gastritis risk and gastric cancer prognosis

2017
Oncotarget
PMCID: 5707023
PMID: 29221129
DOI: 10.18632/oncotarget.20115

[…] biological process (BP) and molecular function (MF). Consequently, some lncRNAs were suggested to possibly contribute to AG initiation. For lnc-LRFN2-1, several co-expressing genes were found through Multi Experiment Matrix (MEM) []. GO analysis demonstrated they might target plasma membrane, concentrating on ion transport, channel activity and detection of external stimulus. Three co-expressing g […]

call_split

Clinical Significance and Effect of lncRNA HOXA11 AS in NSCLC: A Study Based on Bioinformatics, In Vitro and in Vivo Verification

2017
Sci Rep
PMCID: 5514100
PMID: 28717185
DOI: 10.1038/s41598-017-05856-2
call_split See protocol

[…] To further analyze the potential pathways associated with HOXA11-AS, we used an open-access resource, Multi Experiment Matrix (MEM, http://biit.cs.ut.ee/mem/index.cgi), , to interactively explore the co-expressed genes for HOXA11-AS based on an Affymetrix Gene Chip Human Genome U133 Plus 2.0 Array pla […]

Citations

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MEM institution(s)
Institute of Molecular and Cell Biology, Tartu, Estonia; Institute of Computer Science, University of Tartu, Tartu, Estonia; Quretec, Tartu, Estonia
MEM funding source(s)
Supported by EU FP6 grants (ENFIN LSHG-CT-2005-518254 and COBRED LSHB-CT-2007-037730), ERDF through the Estonian Centre of Excellence in Computer Science project and Estonian Science Foundation ETF7427, and Ustus Agur and Artur Lind foundations.

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