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PANOGA specifications

Information


Unique identifier OMICS_02238
Name PANOGA
Alternative name Pathway and Network Oriented GWAS Analysis
Interface Web user interface
Restrictions to use None
Input data PANOGA accepts GWAS results including reference SNP ID.
Output data PANOGA outputs SNP-targeted pathway and gene tables and customized pathway maps.
Programming languages Java, PHP
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publication for Pathway and Network Oriented GWAS Analysis

PANOGA citations

 (6)
library_books

In silico analyses and global transcriptional profiling reveal novel putative targets for Pea3 transcription factor related to its function in neurons

2017
PLoS One
PMCID: 5291419
PMID: 28158215
DOI: 10.1371/journal.pone.0170585

[…] transactivator from binding when Pea3-VP16 was bound.To identify the impact of these changes at cellular level and determine the affected pathways, microarray data were further analyzed in 5 runs of PANOGA. These results were then listed from the most statistically significant pathway to the least: Cell cycle, MAPK signaling pathway and Pathways in cancer, Endocytosis and Neurotrophin signaling p […]

library_books

IDH mutant glioma specific association of rs55705857 located at 8q24.21 involves MYC deregulation

2016
Sci Rep
PMCID: 4901315
PMID: 27282637
DOI: 10.1038/srep27569

[…] -allele. However, only limited information could be gathered with this type of candidate based approach. Therefore, we next undertook transcriptomic analysis of tumors followed by network analysis by PANOGA (Pathway and Network Oriented GWAS Approach).To this end, we performed RNA-seq analysis of 6 WHO grade-II tumors (n = 4 with the A/G, n = 2 with the A/A genotype) that were IDH1-R132H mutant, 1 […]

library_books

A novel analysis strategy for integrating methylation and expression data reveals core pathways for thyroid cancer aetiology

2015
BMC Genomics
PMCID: 4682414
PMID: 26678064
DOI: 10.1186/1471-2164-16-S12-S7

[…] ta from different platforms publicly available, Ilknur Melis Durasi for helping at functional enrichment and transcription factor analyses, Burcu Bakir Gungor for providing additional instructions on PANOGA protocol and Vibin Varghese for reviewing the manuscript. Moreover, the project was supported by Republic of Turkey Ministry of Development Infrastructure Grant (no: 2011K120020) and BILGEM - T […]

library_books

CSF Proteomics Identifies Specific and Shared Pathways for Multiple Sclerosis Clinical Subtypes

2015
PLoS One
PMCID: 4420287
PMID: 25942430
DOI: 10.1371/journal.pone.0122045

[…] t stages but also within the same clinical phenotype [, , ] To better understand the disease continuum, a novel systems approach involving analysis of available data in a pathway related context with PANOGA analysis tool, which is a pathway oriented analysis method bringing a systems level approach.Here we aimed to analyze the CSF proteomic profile from a prospective cohort that has been followed […]

library_books

The Identification of Pathway Markers in Intracranial Aneurysm Using Genome Wide Association Data from Two Different Populations

2013
PLoS One
PMCID: 3590201
PMID: 23483893
DOI: 10.1371/journal.pone.0057022

[…] aims to find out active sub-networks in the human PPI network using jActive Modules algorithm . Although this algorithm was originally developed for microarray gene expression data, steps (i)-(v) of PANOGA successfully adapts GWAS data to be used with this algorithm. In terms of GWAS data, the jActive Modules algorithm integrates the network topology with the calculated Pw-values of each gene to […]

library_books

A New Methodology to Associate SNPs with Human Diseases According to Their Pathway Related Context

2011
PLoS One
PMCID: 3201947
PMID: 22046267
DOI: 10.1371/journal.pone.0026277

[…] Starting with 25,176 SNPs, that are found to be significant in a GWAS (WTCCC RA dataset), PANOGA was performed to identify RA related genes and functionally important KEGG pathways. These SNPs were assigned into 4,029 genes using SPOT webserver by considering all known SNP/gene transcript […]

Citations

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PANOGA institution(s)
Department of Genetics and Bioinformatics, Faculty of Arts and Sciences, Bahcesehir University, Besiktas, Istanbul, Turkey; Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Abdullah Gul University, Kayseri, Turkey; Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey; Department of Biological Sciences and Bioengineering, Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey
PANOGA funding source(s)
This work has been supported by the Abdullah Gul University Support Foundation (AGUV).

PANOGA reviews

 (2)
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Anonymous user #5814

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The link to the Panoga website does not work. 2016-10-14
Anonymous user #4141's avatar image No country

Anonymous user #4141

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Web
Hello.. myself seema , research scholar from DIPAS, DRDO , actually wants to user this PANOGA tool for my research data analysis. but the official site (http://panoga.sabanciuniv.edu/) given in not openning..