Identification and characterization of genes associated with IBD on chromosomal region 1q32
Bibliographic record
Abstract
Crohn's disease (CD) is an inflammatory bowel disease (IBD) characterized by chronic inflammation. This complex trait disease appears to be the result of immune system deregulation. Genome-wide association studies (GWAS) have improved our understanding of the molecular pathways leading to IBD. A meta-analysis combining three GWASconfirmed 11 loci and identified an additional 21 new regions that contribute to Crohn's disease susceptibility (Barrett JC et al., 2008). One of these newly identified loci associated on chromosome 1q32 contains at least four genes: Chromosome 1 open reading frame 81 (C1orf81), Chromosome 1 open reading frame 106 (C1orf106), Kinesin family member 21B (KIF21B) and Calcium channel, voltage-dependant, L type, alpha 1S subunit (CACNA1S). This region has also been shown to be a susceptibility locus in ulcerative colitis (Anderson CA et al., 2009). The challenge is to put these four genes in a biological context to determine the one(s) that is important in IBD. First, using quantitative PCR, we examined the candidate genes expression in murine tissues and also in inflamed and non-inflamed biopsies from CD and non-IBD patients to determine the gene expression in tissues related to IBD. Second, we examined gene expression in immune cells lines to define an appropriated cell model for functional studies. Preliminary data show that the calcium channel, CACNA1S, is almost exclusively expressed in muscle tissues. The novel protein, C1orf106, showed a higher expression in thymus and intestine and a lower expression in inflamed intestinal biopsies compare to non-inflamed and control tissues. KIF21B showed a higher expression in brain, thymus, intestine and inflamed intestinal biopsies. Multiple primers were tested in different tissues and cell lines and expression may be limited, which agrees with expressed sequence tag data. Based on expression studies, these preliminary data suggest that CACNA1S and C1orf81 are not involved in Crohn's disease and that KIF21B and C1 or f106 are still candidate genes which will need more functional studies to determine their role in the Crohn's disease pathogenesis. This work was supported by grants from the NIDDK and the CCFA.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".