SchizPrioritizer

This application allows the prioritization of genes within schizophrenia candidate gene regions (SCRs), specifically within subregions, by assigning weights to various parameters specified below. The genetic locations of the SCRs were projected onto the high resolution Rutgers third-generation combined linkage-physical map (Rutgers Map v.3). You may change the weights assigned to the different parameters and indicate the cut-off based on the weights before running SchizPrioritizer.

The values of x for the SCR subregions below correspond to the maximum -log₁₀(p-values) that we have calculated from our simulations as part of our smoothing method. A higher value of x corresponds to a higher LOD score obtained from our integrated analysis of 47 independent genomewide linkage scans for SZ. "Outside" a specific genetic element (e.g., segmental duplication), includes region 10kb upstream or downstream of that element. The percentage (%) cut-off will be used to determine the exact cut-off score for the genes that will be included in the output file. This means that if other genes below the percentage cut-off have the same overall score as the gene at the cut-off %, we will include those genes in the results page.

Note: This page is still under construction. This will be available soon.

CRITERIA		ASSIGNED WEIGHT
SCR Subregions (x = -log10(p-value); class size=0.2988):
Class 1: 2.1397 ≤ x
Class 2: 1.8409 ≤ x < 2.1397
Class 3: 1.5421 ≤ x < 1.8409
Class 4: 1.2433 ≤ x < 1.5421
Class 5: 0.9445 ≤ x < 1.2433
Class 6: 0.6457 ≤ x < 0.9445
Class 7: 0.3469 ≤ x < 0.6457
Annotated at SZGene (association studies and meta-analyses)    where ratio = positive results / negative results:
Without a negative result
At least five positive results
One to four positive results
At least one negative result
At least ten positive results and ratio ≥ 5.00
At least two positive results and ratio ≥ 5.00
At least five positive results when ratio ≤ 5.00
Without a positive result but annotated at SZGene
Differentially Expressed Genes in SZ Microarray Studies:
Significant result and validated
Nominal significance
Phenotypes/Diseases:
Have SZ as one of its phenotypes
Have an associated phenotype aside from SZ
Structural Variations:
Segmental Duplications (SDs)
Within SDs
Outside SDs
Copy Number Variations (CNVs)
Within CNVs
Outside CNVs
Rearrangement Hotspots
Within hotspots
Outside hotspots
Regulatory Elements (CpG Islands, ORegAnno REs, TargetScan miRNA     regulatory sites, HMR Conserved TF binding sites, Vista enhancers):
Within Regulatory Regions
Outside Regulatory Regions
Functional Noncoding RNAs (miRNAs):
Within miRNAs
Outside miRNAs

Cut-off (specify the top % genes that will be used to determine the cut-off score):  



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