PILNC (Pharmacogenomic and Immune landscape of LncRNA) is a database to provide a comprehensive resource of pharmacogenomic and immune landscape of long non-coding RNAs for human cancers in TCGA.
In PILNC, we provide following data queries:
1) Browse or search associations between lncRNAs and cancer signaling pathway across human cancers;
2) Browse or search associations between lncRNAs and imputed drug responses across human cancers;
3) Browse or search associations between lncRNAs and immune checkpoints across human cancers;
4) Browse or search associations between lncRNAs and different types of immune cell infiltration across human cancers;
5) Browse or search lncRNAs associated with irAE;
6) Browse or search lncRNAs associated with immunotherapy response.
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1) Pathway module: collected lncRNAs which are significantly (|Spearman's correlation| > 0.3, FDR < 0.05) associated with cancer signaling pathways across human cancers.
2) Drug response module: collected lncRNAs which are significantly (|Spearman's correlation| > 0.3, FDR < 0.05) associated with imputed drug response from DrVAEN and CancerRxTissue sources across human cancers.
3) Immune Checkpoint module: collected lncRNAs which are significantly (|Spearman's correlation| > 0.3, FDR < 0.05) associated with immune checkpoint genes across human cancers.
4) Immune Infiltration module: collected lncRNAs which are significantly (|Spearman's correlation| > 0.3, FDR < 0.05) associated with immune cell abundance across human cancers.
5) Immunotherapy Response module: collected lncRNAs which are associated with immunotherapy objective response rate (ORR) or differentially expressed in low and high ORR cancer groups.
6) irAE module: collected lncRNAs which which are associated with irAE reporting odds ratio (ROR) or differentially expressed in low and high ROR cancer groups.
| Cancer Type | Number of samples | Number of lncRNAs | LncRNA-Pathway pairs | LncRNA-Imputed drug response pairs (VAEN) | LncRNA-Imputed drug response pairs (CancerRxTissue) | LncRNA-Immune checkpoint pairs | LncRNA-Immune Cell pairs (TIMER) | LncRNA-Immune Cell pairs (CIBERSORT) | LncRNA-Immune Cell pairs (CIBERSORT.ABS) | LncRNA-Immune Cell pairs (QUANTISEQ) | LncRNA-Immune Cell pairs (MCPCOUNTER) | LncRNA-Immune Cell pairs (XCELL) | LncRNA-Immune Cell pairs (EPIC) | LncRNA-Immune Cell pairs (ImmuCellAI) | LncRNA-Immune Cell pairs (GSVA) | Immunotherapy Objective Response Rate (ORR) | irAE Reporting Odds Ratio (ROR) |
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