Dataset Information

Identify lymphatic metastasis-associated genes in mouse hepatocarcinoma cell lines using gene chip.

ABSTRACT: AIM:In order to obtain lymphogenous metastasis-associated genes, we compared the transcriptional profiles of mouse hepatocarcinoma cell lines Hca-F with highly lymphatic metastasis potential and Hca-P with low lymphatic metastasis potential. METHODS:Total RNA was isolated from Hca-F and Hca-P cells and synthesized into double-stranded cDNA. In vitro transcription double-stranded cDNA was labeled with biotin (i.e. biotin-labeled cRNA, used as the probe). The cRNA probes hybridized with Affymetrix GeneChip(r) MOE430A (containing 22 690 transcripts, including 14 500 known mouse genes and 4 371 ESTs) respectively and the signals were scanned by the GeneArray Scanner. The results were then analyzed by bioinformatics. RESULTS:Out of the 14 500 known genes investigated, 110 (0.8%) were up regulated at least 2(3) fold. Among the total 4 371 ESTs, 17 ESTs (0.4%) (data were not presented) were up regulated at least 2(3) fold. According to the Gene Ontology and TreeView analysis, the 110 genes were further classified into two groups: differential biological process profile and molecular function profile. CONCLUSION:Using high-throughput gene chip method, a large number of genes and their cellular functions about angiogenesis, cell adhesion, signal transduction, cell motility, transport, microtubule-based process, cytoskeleton organization and biogenesis, cell cycle, transcription, chaperone activity, motor activity, protein kinase activity, receptor binding and protein binding might be involved in the process of lymphatic metastasis and deserve to be used as potential candidates for further investigation. Cyclin D1, Fosl1, Hsp47, EGFR and AR, and Cav-1 are selected as the possible candidate genes of the metastatic phenotype, which need to be validated in later experiments. ESTs (data were not presented) might indicate novel genes associated with lymphatic metastasis. Validating the function of these genes is helpful to identify the key or candidate gene/pathway responsible for lymphatic metastasis, which might be used as the diagnostic markers and the therapeutic targets for lymphatic metastasis.

SUBMITTER: Song B

PROVIDER: S-EPMC4305688 | biostudies-literature | 2005 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Identify lymphatic metastasis-associated genes in mouse hepatocarcinoma cell lines using gene chip.

Song Bo B Tang Jian-Wu JW Wang Bo B Cui Xiao-Nan XN Hou Li L Sun Lu L Mao Li-Min LM Zhou Chun-Hui CH Du Yue Y Wang Li-Hui LH Wang Hua-Xin HX Zheng Ren-Shu RS Sun Lei L

World journal of gastroenterology 20050301 10

<h4>Aim</h4>In order to obtain lymphogenous metastasis-associated genes, we compared the transcriptional profiles of mouse hepatocarcinoma cell lines Hca-F with highly lymphatic metastasis potential and Hca-P with low lymphatic metastasis potential.<h4>Methods</h4>Total RNA was isolated from Hca-F and Hca-P cells and synthesized into double-stranded cDNA. In vitro transcription double-stranded cDNA was labeled with biotin (i.e. biotin-labeled cRNA, used as the probe). The cRNA probes hybridized ...[more]

PMID: 15770722

Similar Datasets

Project description:BackgroundChIPx (i.e., ChIP-seq and ChIP-chip) is increasingly used to map genome-wide transcription factor (TF) binding sites. A single ChIPx experiment can identify thousands of TF bound genes, but typically only a fraction of these genes are functional targets that respond transcriptionally to perturbations of TF expression. To identify promising functional target genes for follow-up studies, researchers usually collect gene expression data from TF perturbation experiments to determine which of the TF targets respond transcriptionally to binding. Unfortunately, approximately 40% of ChIPx studies do not have accompanying gene expression data from TF perturbation experiments. For these studies, genes are often prioritized solely based on the binding strengths of ChIPx signals in order to choose follow-up candidates. ChIPXpress is a novel method that improves upon this ChIPx-only ranking approach by integrating ChIPx data with large amounts of Publicly available gene Expression Data (PED).ResultsWe demonstrate that PED does contain useful information to identify functional TF target genes despite its inherent heterogeneity. A truncated absolute correlation measure is developed to better capture the regulatory relationships between TFs and their target genes in PED. By integrating the information from ChIPx and PED, ChIPXpress can significantly increase the chance of finding functional target genes responsive to TF perturbation among the top ranked genes. ChIPXpress is implemented as an easy-to-use R/Bioconductor package. We evaluate ChIPXpress using 10 different ChIPx datasets in mouse and human and find that ChIPXpress rankings are more accurate than rankings based solely on ChIPx data and may result in substantial improvement in prediction accuracy, irrespective of which peak calling algorithm is used to analyze the ChIPx data.ConclusionsChIPXpress provides a new tool to better prioritize TF bound genes from ChIPx experiments for follow-up studies when investigators do not have their own gene expression data. It demonstrates that the regulatory information from PED can be used to boost ChIPx data analyses. It also represents an important step towards more fully utilizing the valuable, but highly heterogeneous data contained in public gene expression databases.

Dataset Information

Identify lymphatic metastasis-associated genes in mouse hepatocarcinoma cell lines using gene chip.

Publications

Identify lymphatic metastasis-associated genes in mouse hepatocarcinoma cell lines using gene chip.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets