Tutorial: DOCX/PDF
Video Introduction MP4/OGG

Interpretation Guide

Source: https://github.com/UcarLab/QuIN/ (License)

Data/Database:
Data for Clinvar, dbSNP (GRCH37.p13), NCBI Gene Databases (gene2go & gene2refseq), The GWAS Catalog and UCSC hg19 Refflat Database last updated on 5/3/2016.

Data for preloaded ENCODE datasets last updated on 6/30/2015.

GEO Accessions For Preloaded Datasets:
MCF-7 Pol2 ChIAPET - GSM970209
MCF-7 H3K4me3 - GSM945269
MCF-7 H3K27ac - GSM945854

K562 Pol2 ChIAPET - GSM970213
K562 H3K4me3 - GSM733680
K562 H3K27ac - GSM733656


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Component:  

Layout:
 
 
 
 

GO Enrichment Analysis
 
 
 
Network Statistics
Component Statistics
Legend
 
No Network Selected
Number of Components
 
Number of Nodes
 
Number of Edges
 
Average PET per Edge
 


Parameters
Extend
 
Minimum PET per Edge
 
Interaction Type
 
Max Intrachromosome Distance
 
Minimum Component Size
 
Maximum Component Size
 
 
 
Network measures over all components. Values are normalized with respect to their component.

Degree:

Closeness:

Harmonic:

Betweenness:
Background Type:
Distance Cutoff:
Instead of assuming every node can be connected by an edge, the intrachromosome theoretical model computes the total number of possible edges within the chromosome while also using a distance criteria for any hard limits put in place (i.e., 1MB) such that nodes with a distance larger than this cut off will not contribute to adding an edge to the total possible edges.
Number of Permutations (1-100000):

 
General Information
Location:
PET Count/score:
 
Interaction Count:
 
Centrality Measures
Type
Non-Normalized
Network Normalized
Component Normalized
Degree
 
 
 
Closeness
 
 
 
Harmonic
 
 
 
Betweenness
 
 
 
General Information
Inner Span:
 
Outer Span:
 
Location 1:
 
Location 2:
 
PET Count/Score:
 
Interaction Count:
 
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