IPAfunc logo - IPAfunc is a knowledgebase for functional annotations of intronic polyadenylation in human cancers. IPAfunc reveals the IpA events associated with cancer survival and tumor progression. Moreover, the potential downstream effects of IpA on gene/isoform expression, regulation of miRNAs, RNA binding proteins (RBPs), and alternative splicing events are included in IPAfunc. In addition, IPAfunc also reveals the upregulators of IpA events, such as the effects of genetic variants on intronic poly(A) sites and RBPs, as well as the effect of methylation phenotypes on IpA events.

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1. IPAfunc information
2. Understanding annotation of IPAfunc
    a. Search by gene symbol or IpA ID, example: Gene symbol: AACS, IpA ID: chr12:125622275:+AACS
    b. Gene search result page
    c. IPAfunc annotation result page
        i. Summary of IpA events by genes
        ii. Associations of IpA events and isoform expression
        iii. Associations of IpA events and gene expression
        iv. Stage-specific differential IpA events
        v. Prognosis-related IpA events
        vi. IpA-regulated miRNA escape
        vii. Effect of IpA events in splicing factors on alternative splicing
        viii. IpA events Quantitative Trait Methylation (IpAQTM)
        ix. Effect of IpA events in RBPs on their targets
        x. IpA events dysregulated by SNPs
        xi. IpA events associated immune infiltration
        xii. IpA events related FDA approved-drugs
        xiii. IpA events contribute to drug resistance
3. Download data and contact us

bullet point 1. IPAfunc information
IPAfunc reveals the upregulators of IpA events, such as the effects of genetic variants on intronic poly(A) sites and RBPs, as well as the effect of methylation phenotypes on IpA events. These findings demonstrate that IPAfunc is a useful resource for better understanding IpA and their potential functions in cancer biology.

bullet point 2. Understanding annotation of IPAfunc
bullet point a. Search by gene symbol or IpA ID, example: Gene symbol: AACS, IpA ID: chr12:125622275:+AACS
      - Input query: Gene symbol.
Search page of AACS - An image showing the gene search bar of searching example gene AACS. The user can search the gene via gene symbol AACS or IpA ID chr12:125622275:+AACS

bullet point b. Gene search result page
 This image shows the gene list according to your search.
Search result of AACS - An image showing the search result of AACS, including Gene Symbol, Gene Synonym, Gene Description, Gene Type and IpA ID. Gene Symbol is AACS, Gene Synonym is C14orf41|S171|c14_5527, Gene Description is AACS_homolog_(Drosophila)_[Source:HGNC_Symbol;Acc:8060], Gene Type is protein_coding and IpA ID is chr12:125622275:+AACS; chr14:73748127:-AACS; chr14:73875622:-AACS.

bullet point c. IPAfunc annotation result page
 This image shows IPAfunc's annotation categories for your query with links to their corresponding annotation parts.
Annotation of IPAfunc includes Summary of IpA events by genes, Associations of IpA events and isoform expression, Associations of IpA events and gene expression, Stage-specific differential IpA events, Prognosis-related IpA events, IpA-regulated miRNA escape, Effect of IpA events in RBPs on their targets, IpA events dysregulated by SNPs and IpA events related FDA approved-drugs.

bullet point i. 'Summary of IpA events by genes' category
This image category shows the information of the IPAfunc.
Summary of AACS - An image showing the overall information of AACS such as Gene Symbol, Gene Synonym, Gene Description, Gene Type and IpA ID. Gene Symbol is AACS, Gene Synonym is C14orf41|S171|c14_5527, Gene Description is AACS_homolog_(Drosophila)_[Source:HGNC_Symbol;Acc:8060], Gene Type is protein_coding and IpA ID is chr12:125622275:+AACS; chr14:73748127:-AACS; chr14:73875622:-AACS.

bullet point ii. 'Associations of IpA events and isoform expression' category
This image category provides the associations of IpA events and isoform expression.
                   Note: There is no result of AACS in this category. Here is the result of C1orf159 as an example.
Associations of IpA events and isoform expression - An image showing the result of IpA events and isoform expression, it gives the basic information of the result, including Gene Symbol, IpA ID, isoform id, r_val, p_val, FDR and Cancer Type
bullet point iii. 'Associations of IpA events and gene expression' category
This image category provides the associations of IpA events and gene expression.
Associations of IpA events and gene expression - An image showing the result of IpA events and gene expression, it gives the basic information of the result, including Gene Symbol, IpA ID, isoform id, r_val, p_val, FDR and Cancer Type

bullet point iv. 'Stage-specific differential IpA events' category
This image category provides the stage-specific differential IpA events.
stage-specific differential IpA events of AACS - An image showing the result of stage-specific differential IpA events of AACS, it gives the basic information including Gene Symbol, IpA ID, p value of StageI_StageII, StageI_StageIII, StageI_StageIV, StageII_StageIII, StageII_StageIV ,StageIII_StageIV and Cancer Type.
bullet point v. 'Prognosis-related IpA events' category
This image category provides the prognosis-related IpA events.
                   Note: There is no result of AACS in this category. Here is the result of CASZ1 as an example.
prognosis-related IpA events - An image showing the analysis result of prognosis-related IpA events, it gives the basic information including Gene Symbol, IpA ID, Survival p_val and Cancer Type.

bullet point vi. 'IpA-regulated miRNA escape' category
This image category provides the IpA-regulated miRNA escape.
IpA-regulated miRNA escape of AACS - An image showing the analysis result of IpA-regulated miRNA escape, it gives the basic information including Gene Symbol, miRNA Family ID, miRNA Binding Site Loci, Site Type and Cancer Type.

bullet point vii. 'Effect of IpA events in splicing factors on alternative splicing' category
This image category provides the effect of IpA events in splicing factors on alternative splicing.
Effect of IpA events in RBPs on their targets - An image showing the analysis result of effect of IpA events in RBPs on their targets, it gives the basic information including Gene Symbol, IpA ID, RBP, RBP IPA ID, Target Gene, Target Gene IPA ID, r_val, p_val and Cancer Type.

bullet point viii. 'IpA events Quantitative Trait Methylation (IpAQTM)' category
This image category provides IpA events Quantitative Trait Methylation (IpAQTM).
IpA events dysregulated by SNPs - An image showing the analysis result of IpA events dysregulated by SNPs, it gives the basic information including Gene Symbol, IpA ID, rs_id, ref, alt, hexamers_ref, hexamers_alt, snp_affect_pas and variant_position. It shows the result of SNPs_affect_PAS and SNPs_affect_PAS_reverse in This image category.

bullet point ix. 'Effect of IpA events in RBPs on their targets' category
This image category provides Effect of IpA events in RBPs on their targets.
Related IpA events and drug information of AACS - An image showing the IpA events related FDA approved-drugs, it gives the basic information including Gene Symbol, IpA ID, UniProtAcc, DrugBank ID, Drug name, Drug Activity, Drug Type and Drug Status

bullet point x. 'IpA events dysregulated by SNPs' category
This image category provides IpA events dysregulated by SNPs.
Related IpA events and drug information of AACS - An image showing the IpA events related FDA approved-drugs, it gives the basic information including Gene Symbol, IpA ID, UniProtAcc, DrugBank ID, Drug name, Drug Activity, Drug Type and Drug Status

bullet point xi. 'IpA events associated immune infiltration' category
This image category provides IpA events associated immune infiltration.
Related IpA events and drug information of AACS - An image showing the IpA events related FDA approved-drugs, it gives the basic information including Gene Symbol, IpA ID, UniProtAcc, DrugBank ID, Drug name, Drug Activity, Drug Type and Drug Status

bullet point xii. 'IpA events related FDA approved-drugs' category
This image category provides IpA events related FDA approved-drugs.
                   Note: There is no result of AACS in this category. Here is the result of A1BG as an example.
Related IpA events and drug information of AACS - An image showing the IpA events related FDA approved-drugs, it gives the basic information including Gene Symbol, IpA ID, UniProtAcc, DrugBank ID, Drug name, Drug Activity, Drug Type and Drug Status

bullet point xiii. 'IpA events contribute to drug resistance' category
This image category provides IpA events contribute to drug resistance.
Related IpA events and drug information of AACS - An image showing the IpA events related FDA approved-drugs, it gives the basic information including Gene Symbol, IpA ID, UniProtAcc, DrugBank ID, Drug name, Drug Activity, Drug Type and Drug Status

bullet point 3. Download data and contact us
Please go to download page and contact page.