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Transcript 
Colon Cancer in-house Database
(Atlantic Project)
Lucila
Machado
Enrico Capobianco
Simone Carcangiu
Kim Jihonn
Massimiliano Orsini
Mark
Epitzer
Antonella
Travaglione
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 …
CRC
(colorectal cancer pilot study case)
Array Express
Transcripts
by gene
Expressions
Raw
Normalized
DISEASE
ASSOCIATION
Steps
Samples:
 User-friendly complete annotation
Genes:

Genome probe mapping
Expressions:
 Prediction/Classification Models
Today Focus
Curation of the transcriptome warehouse
Array Express
Colon cancer, colorectal cancer, colorectal tumor…
Experimental information
Sample information
Sample annotation from our partners
(GEO based)
• Inserire loro campi
Our sample annotation
building blocks
• Cell information
• Cancer information
• Patient information
• Risk factors
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..
- Disease staging: duke's B primary, duke's C etc..
- Developmental Stage: adult, fetal
- Tumor size
- Clinical history: high metastatic activity, low metastatic activity
Our sample fields
3. Patient information
- Age : 0-100
- 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
- FAP Familial adenomatous polyposis
- HNPCC Hereditary Non-Polyposis Colon Cancer (Lynch Syndrome)
- Smooking
- Alcohol
- Caffeine
- Diabetes
DB scheme
Next Steps
Genes:

Genome probe mapping
Expressions:
 Prediction/Classification Models
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