Identification of New Colorectal Cancer Genes
Ontology highlight
ABSTRACT:
DISEASE(S): Colorectal Cancer,Colorectal Neoplasms
PROVIDER: 2048176 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
Similar Datasets
Project description:RATIONALE: Identification of genes that may be associated with developing certain types of cancer may someday provide important information about a person’s risk of getting cancer.
PURPOSE: This clinical trial is studying to see if certain genes may be associated with cancer in patients with cancer of the breast, prostate, lung, or colon and siblings of these patients.
| 2002870 | ecrin-mdr-crc
Project description:Examination of cRNA from Arabidopsis flowers, roots and suspension cell culture using custom high-density Affymetrix genome tiling arrays in order to identify new and unpredicted genes. Keywords: other
2003-10-30 | GSE601 | GEO
Project description:Identification of new and unpredicted full length Arabidopsis genes. Examination of cRNA prepared from Arabidopsis thaliana ecotype Columbia light grown 7-day old seedlings using whole genome tiling arrays. Keywords: other
2003-10-30 | GSE605 | GEO
Project description:There is clear evidence that clinical genetic counseling for hereditary cancer saves lives and relieves anxiety. Our aim is to identify novel genes that predispose to familial colorectal cancer. We follow the empirical gene discovery paradigm by identifying high-risk families diagnosed with the same cancer in several family members. Such families and samples are identified from the world’s largest biobank of 16,000 familial cancers in Szczecin. For this study we identified 15 colorectal cancer families with several affected family members. Germline DNA from cases and unaffected family members are sequenced genome-wide at the DKFZ core facility, one of Europe’s top sequencing centers. Based on the proof-of-principle study on melanoma, a single family may allow identification of a high-risk variant when the new genome-wide sequencing technology is applied. In that example, the detected variant targeted a transcription factor binding site which turned out to be the most common gene variant in melanoma yet described, with implications to prognosis. The present project aims at cancer prevention in identifying novel high-risk variants for which predictive gene testing can be established.
| EGAS00001005118 | EGA
Project description:Since the worldwide increase in obesity represents a growing challenge for the health care systems, new approaches are needed to treat obesity and associated disease effectively. The food intake is primarily stored in the adipose tissue and therefore this organ is in focus to develop new anti-obesity treatments. To provide a systematic analysis of genes that regulate adipose tissue biology and to establish a target-oriented compound screening, we performed a high throughput siRNA screen with primary (pre)adipocytes, using a druggable siRNA library targeting 7,784 human genes. Beside well known regulators of adipogenesis and neutral lipid storage (like PPAR?, RXR, Perilipin A) the screening revealed a large number of genes which were not previously described in the context of fatty tissue biology. An enrichment of genes was observed for axonemal dyneins. Five out of ten anxonemal dyneins were identified in our primary screen and retested positive with independent siRNAs and cell-donors. Quantitative RT-PCR- and immunoblot analysis revealed that axonemal dyneins are expressed in preadipocytes and maturing adipocytes. Using microarray analysis, we further characterize the remaining genes identified in our primary screen to determine their expression pattern during adipogenesis. In the course of fat cell differentiation, 149 among the 459 positive genes were regulated on the gene expression level. Assuming that an adipogenesis-specific expression pattern is another independent hind, that these genes are involved in neutral lipid storage and/or adipocyte differentiation, we retested this gene-pool with independent siRNAs and cell donors. Finally, to show that the genes identified are per se druggable we performed a proof of principle experiment using an antagonist for one randomly chosen gene. The results showed a very similar phenotype compared to knock-down experiments proofing the druggability. Thus, we identified new adipogenesis-associated genes and those involved in neutral lipid storage. Moreover, by using a druggable siRNA library the screen data provides a very attractive starting point, to identify anti-obesity compounds targeting the adipose tissue.
2012-03-06 | GSE28628 | GEO
Project description:Since the worldwide increase in obesity represents a growing challenge for the health care systems, new approaches are needed to treat obesity and associated disease effectively. The food intake is primarily stored in the adipose tissue and therefore this organ is in focus to develop new anti-obesity treatments. To provide a systematic analysis of genes that regulate adipose tissue biology and to establish a target-oriented compound screening, we performed a high throughput siRNA screen with primary (pre)adipocytes, using a druggable siRNA library targeting 7,784 human genes. Beside well known regulators of adipogenesis and neutral lipid storage (like PPAR?, RXR, Perilipin A) the screening revealed a large number of genes which were not previously described in the context of fatty tissue biology. An enrichment of genes was observed for axonemal dyneins. Five out of ten anxonemal dyneins were identified in our primary screen and retested positive with independent siRNAs and cell-donors. Quantitative RT-PCR- and immunoblot analysis revealed that axonemal dyneins are expressed in preadipocytes and maturing adipocytes. Using microarray analysis, we further characterize the remaining genes identified in our primary screen to determine their expression pattern during adipogenesis. In the course of fat cell differentiation, 149 among the 459 positive genes were regulated on the gene expression level. Assuming that an adipogenesis-specific expression pattern is another independent hind, that these genes are involved in neutral lipid storage and/or adipocyte differentiation, we retested this gene-pool with independent siRNAs and cell donors. Finally, to show that the genes identified are per se druggable we performed a proof of principle experiment using an antagonist for one randomly chosen gene. The results showed a very similar phenotype compared to knock-down experiments proofing the druggability. Thus, we identified new adipogenesis-associated genes and those involved in neutral lipid storage. Moreover, by using a druggable siRNA library the screen data provides a very attractive starting point, to identify anti-obesity compounds targeting the adipose tissue. For microarray analysis, RNA was isolated at 3 different points in time during adipogenesis (day 0, day 3 and day 7 after induction of differentiation). This experiment was carried out with cells obtained from three different donors. No replicates are included for each point in time.
2012-03-06 | E-GEOD-28628 | biostudies-arrayexpress
Project description:Identification of new and unpredicted full length Arabidopsis genes. Examination of cRNA prepared from Arabidopsis thaliana ecotype Columbia light grown 7-day old seedlings, light grown 7-day old seedlings treated at 4 degrees C for 24hrs, and etiolated 7-day old seedlings using pilot genome tiling arrays. Total RNA was isolated from seedlings with the TRIzol reagent procedure of Invitrogen, then poly(A)+ RNA was purified with Qiagen oligotex. One microgram poly(A)+ RNA was converted into ds-cDNA using T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions using ENZO labeling kit, fragmented and then 20 micrograms of fragmented cRNA were hybridized to the arrays according to Affymetrix instructions. Keywords: other
2003-10-30 | GSE604 | GEO
Project description:Transposon mutagenesis screens in mice has allowed us the identification of new tumor suppressor genes in cancer. To further explore the mechanistic role of these genes at the molecular level, we decided to study the transcriptome of human immortalized and cancer cells which underwent siRNA-mediated silencing of these tumor suppressors. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2016-02-17 | E-ERAD-432 | biostudies-arrayexpress
Project description:The largest family of p97 cofactors is the UBXD protein family, whose members all carry an Ubiquitin Regulatory X (UBX) domain that enables binding to p97. We analysed one member of this family, the largely uncharacterised UBXD9 protein. To shed a light on the UBXD9 interactome, we used independent approaches to identify new interacting proteins. As a result, we confirmed p97 (also known as valosin-containing protein, VCP) as an interaction partner of UBXD9 and identified new interaction partners.
2021-08-26 | PXD027162 | Pride
Project description:Twenty-three family trios of placental cDNA, placental genomic DNA (gDNA) and gDNA from both parents were tested using Illumina SNP arrays to find new imprinted genes to ascertain the extent of allele specific expression in this tissue.
2010-04-15 | E-TABM-796 | biostudies-arrayexpress