Welcome to Help Page

This page provides help to the users of CancerLivER on how to efficiently use this repository. For each module which is implemented in CancerLivER, here we provide the figures and description on how to use that module.

DATASET	BIOMARKER	ANALYSIS
Keyword Search Complex Search Browse by Profiling technique Browse by Disease Browse by type of transcripts	Keyword search Complex search Browse by gene/protein Browse by Biomarker type Browse by Biomolecule Browse by source	Single gene Multiple gene Pathway GO term

Dataset module

Keyword Search
This module displays the simple search page of Dataset module in CancerLivER. Clicking on the required field will allow the user to browse the specific information in the database. The "select fields to be searched" section provides options for various keywords through which search can be made in CancerLivER. User can select fields to be displayed from the section "fields to be displayed". User can click on each cancerLivER ID to get all the details about a entry.

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Complex Search
This page provides the advanced search facility in CancerLivER. User can browse the page by selecting two or more than two fileds.

Complex Search is quite helpful when user has predefined query in mind. For instance, User come up with the following questions in mind and wants to SEARCH

1.Select cancer type like Hepatocellular carcinoma.

2. Among the above selected cancer type select package like oligo.

3. Among the above selection criteria, show type of trancript like protein coding.

4. Among the above, select profiling technique like affymetrix array.

By clicking Submit; user can get desired output.

In a similar way, query can be extended using "+" button and reduced using "-" button.

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Browse by profiling technique
This page browse the entries of CancerLivER based on the Profiling Technique (Affymetrix/Illumina/Agilent/High-throughput).

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Browse by Disease
This page display number of datasets in each types of cancer liver disease (HCC/Cholangiocarcinoma/Fibrolamellar Carcinoma/Heptoblastoma).

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Browse by type of trancripts
This page provides the option to browse the entries of CancerLivER based on the Types of transcripts (Coding/Non-coding/both).

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Biomarker module

Keyword Search
This module displays the simple search page of biomarker module in CancerLivER. Clicking on the required field will allow the user to browse the specific information in the database. The "select fields to be searched" section provides options for various keywords through which search can be made in CancerLivER. User can select fields to be displayed from the section "fields to be displayed". User can click on each cancerLivER ID to get all the details about a entry.

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Complex Search
This page provides the advanced search facility in CancerLivER. User can browse the page by selecting two or more than two fileds.

Complex Search is quite helpful when user has predefined query in mind. For instance, User come up with the following questions in mind and wants to SEARCH

1.Select cancer type like Hepatocellular carcinoma.

2. Among the above selected cancer type select package like oligo.

3. Among the above selection criteria, show type of trancript like protein coding.

4. Among the above, select profiling technique like affymetrix array.

By clicking Submit; user can get desired output.

In a similar way, query can be extended using "+" button and reduced using "-" button.

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Browse by gene/protein
This page provides the option to browse the entries of CancerLivER based on the gene/miRNA.

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Browse by type of biomarkers
This page provides the option to browse the entries of CancerLivER based on the Types of Biomarkers (Diagnostic/Prognostic/Predictive).

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Browse by biomolecule
This page provides the option to browse the biomarkers of CancerLivER based on the type of biomolecule (Protein/RNA/miRNA).

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Browse by source
This page provides the option to browse the entries of CancerLivER based on the Source of Samples from which Biomarkers extracted.

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Analysis Module

Single Gene

Multiple Genes
This module allow the User to analyze the expression profile of multiple genes (selected by users) in expression datasets for selected profile technique. User needs to submit the list of genes in csv format and can analyze them. Further the user can also visualize the centrality measures of each gene for various types of samples in form of box plots and bar graphs.

Pathway
This module allow the User to analyze the expression patterns of genes of a selected pathway in various datasets of Liver cancer samples. User needs to select a pathway (KEGG or Biocarta) and submit for analysis. Further the user can also visualize the centrality measures of each gene for various types of samples in form of box plots and bar graphs.

GO-Term
This module allow the User to analyze the expression patterns of genes of his GO (Gene Ontology) term. User needs to select any GO term (GO_Biological_Process, GO_Cellular Component and GO_Molecular Function) and submit for analyze. Further the user can also visualize the centrality measures of each gene for various types of samples in form of box plots and bar graphs.

Frequently Asked Questions (FAQs)

Q1. What is CancerLivER?
CancerLivER (Liver Cancer Expression Resource) is a database that maintains gene expression datasets of liver cancer along with the putative biomarkers defined for the same in the published literature. It is integrated repository that stores a total of 115 annotated gene expression datasets extracted from GEO (Gene Expression Omnibus) and TCGA (The Cancer Genome Atlas) of 9611 Samples. This resource also store 592 entries of biomarkers for liver cancer retrieved from 153 publications.It also has analysis tools to explore and visualize the expression patterns of desired genes among different types of liver cancer samples in different datasets based on various pathways and GO ontology terms.

Q2. Why CancerLivER?
Ans. It is storehouse of Gene expression datasets and Biomarkers for liver cancer extarcted from Public Repositories and Literature respectively. CancerLivER is a web-based platform to perform search, browsing and analyses of datasets and biomarkers data. This resource is facilitated by an interactive interface to query the datasets and biomarkers along with information like profiling technique, disease condition, type of samples, type of biomarker, patients's cohorts, regulation status of biomarkers etc. Further, CancerLivER has the facility to download annotated expression dataset matrices to facilitate the users for analyzing them in an extensive manner to elucidate more robust Liver cancer specific biomarkers.

Q3. How to search into CancerLivER?
Ans. User can search both Expression Datasets and Putative Biomarker using specific Keywords and by creating a complex query of multiple keywords. Further user can also Browse them based on different categories.