queried for enrichment of the Affymetrix gene sets (биоинформатика) gen.

[dao2812]

Gene set enrichment analysis (GSEA) software (Mootha et al., 2003; Subramanian et al., 2005) was employed to compare genes up- or downregulated in cells stably expressing WT or KR PR to cells expressing inducible iWT or iKR PR. Using the Affymetrix expression data, four gene sets were created: genes up- or downregulated >2.0 fold by iWT with R5020, and genes up- or downregulated >2.0 fold by iKR with R5020. Similarly, two GSEA-formatted datasets were created from the Illumina expression data: the first dataset compares the two phenotypes (WT +R5020 vs WT –R5020), and the second compares the two phenotypes (KR +R5020 vs KR –R5020). GSEA was performed using those Illumina datasets and "queried for enrichment of the Affymetrix gene sets". GSEA was executed using the default settings, except the permutation type was set to Gene_set with 1000 permutations, and the metric for ranking genes was set to Diff_of_Classes because our dataset contained log-scale data.

Gene set enrichment analysis (GSEA) software- программное обеспечение для анализа представленности генов (GSEA)

Спасибо!

[leka11]

см. http://www.med-gen.ru/docs/a_r_Omelchenko DO.pdf
"Gene set enrichment analysis (GSEA) – статистический анализ представленности групп дифференциально экспрессированных генов, соответствующих коллекциям базы данных MSigDB"

[leka11]

http://www.helicon.ru/catalog/spisok.php?IBLOCK_ID=4&SECTION_ID=532
(Микрочиповые системы Affymetrix)

[dao2812]

Спасибо! Все по-отдельности понятно, но: queried for enrichment of the Affymetrix gene sets
Запрашивали...

[leka11]

не "запрашивали",
вероятно, это запрос в базу данных

GSEA was performed using those Illumina datasets and (GSEA was ) queried for enrichment of the Affymetrix gene sets

[dao2812]

Да, но какой запрос? for enrichment of the Affymetrix gene set- как это нормально перевести?

[leka11]

да
см. пример из сети
"....users may select which database types to query for enrichment (e.g. pathway, ontology, protein family). "

[dao2812]

ответ вопросом на вопрос.
Как перевести "query for enrichment"?

[leka11]

"Ну, все, что знал(а) рассказал(а)" :))))), детали - к спецам по теме

[leka11]

м.б. поможет в понимании "enrichment"
см. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605602/
"..an enriched gene set is defined as a set that has significantly higher percentage of DE genes (differentially expressed genes ) than would be expected by chance..."

"A major type of the gene set analysis is to determine whether a pre-defined category of genes is enriched (i.e. over-represented) by DE genes, often referred to as gene set (or pathway) enrichment analysis. A gene set is claimed to be enriched if it contains more DE genes than would be expected by chance..."

[dao2812]

The relative expression of individual PR target genes in human breast tumor samples was determined by searching the Oncomine database (version 4.4, October 2011 data release).

Как перевести genes were queried?
Осуществляли запрос информации о гене?

Individual PR target genes (e.g. RGS2) were queried in The Cancer Genome Atlas (TCGA) Breast 2 dataset

[dao2812]

данных по отдельных генах-мишенях? и тогда запрос данных по представленности генов?

[leka11]

имхо. осуществлялся поиск информации по базе данных