Colon Cancer in-house Database (Atlantic Project) Enrico Capobianco Simone Carcangiu Massimiliano Orsini Antonella Travaglione Lucila Machado Kim Jihonn.

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Presentation transcript:

Colon Cancer in-house Database (Atlantic Project) Enrico Capobianco Simone Carcangiu Massimiliano Orsini Antonella Travaglione Lucila Machado Kim Jihonn Mark Epitzer

Goal Build up-to-date annotated transcriptome warehouse of colon cancer experimental data retrieved from the ArrayExpress db ….various filters apply…. Allow automated flow of gene expression data …

Array Express Transcripts by gene Expressions Raw Normalized DISEASEASSOCIATION CRC (colorectal cancer pilot study case)

Samples:  User-friendly complete annotation Genes:  Genome probe mapping Expressions:  Prediction/Classification Models Steps

Curation of the transcriptome warehouse Today Focus

Colon cancer, colorectal cancer, colorectal tumor… Array Express

Experimental information

Sample information

Inserire loro campi Sample annotation from our partners (GEO based)

Cell information Cancer information Patient information Risk factors Our sample annotation building blocks

Our sample fields 1. Cell information Organism : Homo sapiens Biosource provider : ATCC, DMSZ, DSMZ, ECACC ( Cell Lines Banks) Biosource type: fresh_sample, frozen_sample… Cell line/ Individual (identification code or sample name): SW480, HCT116… Cell type: colon epithelial… Genotype: wild_type… Phenotype: microsatellite instability (MSI-H) Genetically modified : gene_knock_in, gene_knock_out… Treated/ clinical treatment: DMSO.. Treatment type: in vivo, in vitro Treatment time: pre-operative/post-operative.. Time course : 4h…

Our sample fields 2. Cancer information - Organism part: colon, rectum, ascending colon, etc.. - Disease state: colon carcinoma, colon adenocarcinoma;colon cancer,metastasis; colorectal cancer, recurrence etc.. - Tumor size - Disease staging: duke's B primary, duke's C etc.. - Clinical history: high metastatic activity, low metastatic activity - Developmental Stage: adult, fetal

Our sample fields 3. Patient information - Age : Sex: female, male - Race/ ethnicity: Caucasian, African American, etc..

Our sample fields 4. Risk factors information - Family history - Recurrence - Past history of colon cancer - Crohn’s/ulcerative colitis - Diabetes - Smooking - Alcohol - Caffeine - FAP Familial adenomatous polyposis - HNPCC Hereditary Non-Polyposis Colon Cancer (Lynch Syndrome)

DB scheme

Genes:  Genome probe mapping Expressions:  Prediction/Classification Models Next Steps