LncExpDB

Introduction

1 What is LncExpDB?

LncExpDB is a comprehensive database for lncRNA expression. It covers expression profiles of lncRNA genes across various biological contexts, predicts potential functional lncRNAs and their interacting partners, and thus provides essential guidance on experimental design.

Based on comprehensive integration, stringent curation and systematic analysis, LncExpDB currently presents a collection of 101,293 high-quality human lncRNA genes and houses abundant expression profiles derived from 1,977 samples of 337 biological conditions across nine biological contexts. Consequently, LncExpDB estimates lncRNA genes’ expression reliability and capacities, identifies 25,191 featured genes, and further obtains 28,443,865 lncRNA-mRNA interactions.

Moreover, LncExpDB is equipped with user-friendly web interfaces, providing functionalities for data query, browsing, visualization as well as easy access.

Data and Methods

2.1 Data collection

LncExpDB collects a total of 24 RNA-seq datasets across 1,977 samples from GEO, SRA and ArrayExpress, covering 337 biological conditions of nine important biological contexts, including normal tissues/cell lines, organ development, preimplantation embryos, cell differentiation, subcellular localizations, exosomes, cancer cell lines, virus infection and circadian rhythm.

Biological Context	Project ID	Dataset	Source	Sample Number	PMID
Normal Tissue/Cell	E-MTAB-2836	The Human Protein Atlas	EBI ArrayExpress	121	28940711
	SRP013565	ENCODE Primary Cell Lines	NCBI SRA	111	29126249
Organ Development	E-MTAB-6814	Development of Brain	EBI ArrayExpress	55	31243368
	E-MTAB-6814	Development of Cerebellum	EBI ArrayExpress	59	31243368
	E-MTAB-6814	Development of Heart	EBI ArrayExpress	50	31243368
	E-MTAB-6814	Development of Kidney	EBI ArrayExpress	40	31243368
	E-MTAB-6814	Development of Liver	EBI ArrayExpress	50	31243368
	E-MTAB-6814	Development of Ovary	EBI ArrayExpress	18	31243368
	E-MTAB-6814	Development of Testis	EBI ArrayExpress	41	31243368
Preimplantation Embryo	GSE71318	Oocyte to Lateblastocyst (7 Stages)	NCBI GEO	35	27315811
	GSE36552	Oocyte to Lateblastocyst (9 Stages)	NCBI GEO	90	23934149
Cell Differentiation	GSE122380	Cell Differentiation	NCBI GEO	297	31249060
Subcellular Localization	GSE116008	Subcellular Localization	NCBI GEO	36	31230715
Exosome	GSE104926	Blood Exosomes from Early-Stage Esophageal Squamous Cell Carcinoma Patients vs. Normal Control	NCBI GEO	12	32043367
	GSE100063, GSE100206	Blood Exosomes from Colorectal Cancer Patients vs. Normal Control	NCBI GEO	44	30053265
	GSE100063, GSE100206	Blood Exosomes from Coronary Heart Disease vs. Normal Control	NCBI GEO	38	30053265
	GSE100063, GSE100206	Blood Exosomes from Hepatocellular Carcinoma vs. Normal Control	NCBI GEO	53	30053265
	GSE100063, GSE100206	Blood Exosomes from Pancreatic Adenocarcinoma Patients vs. Normal Control	NCBI GEO	46	30053265
Cancer Cell Line	PRJNA523380	Cancer Cell Line	NCBI SRA	658	31068700
Virus Infection	GSE125686	HIV Infection vs. Normal Control	NCBI GEO	22	30185599
	GSE125686	HBV Infection vs. Normal Control	NCBI GEO	48	30185599
	GSE125686	HCV Infection vs. Normal Control	NCBI GEO	24	30185599
	GSE147507	COVID Patients vs. Normal Control	NCBI GEO	4	32416070
Circadian Rhythm	GSE113883	Circadian Rhythm	NCBI GEO	153	30201705
Cancer Immunotherapy	PRJNA482620	Glioblastoma	NCBI SRA	34	29033130
	GSE91061	Melanoma	NCBI GEO	58	30185599
	GSE135222	Non-Small Cell Lung Cancer	NCBI GEO	27	31537801
	GSE181815	Thymic carcinoma	NCBI GEO	8	34622229
Human Aging	GSE104704	Brain	NCBI GEO	18	29507413
	GSE164471	Skeletal Muscle	NCBI GEO	53	33795677
	GSE51518	Skin	NCBI GEO	20	25977295
Metabolic Diseases	GSE162689	Type I Diabetes	NCBI GEO	59	33711030
	GSE153315	Type II Diabetes	NCBI GEO	30	30185599
	GSE244118	Metabolically Healthy / Unhealthy Obesity	NCBI GEO	53	38569471
	GSE254617	Hypertension	NCBI GEO	148	39167456

2.2 Data structure

2.3 Read mapping, quantification and normalization

All samples are processed by a standardized RNA-seq pipeline (Trimmomatic, FastQC, STAR, RSeQC, Kallisto and featureCounts) to get the abundance matrixes (reads count, CPM, FPKM and TPM) of lncRNAs. The raw abundance matrixes are normalized by TMM method.

2.4 Estimation of transcription reliability

LncExpDB considers lncRNA genes with maximum expression values less than 1.0 TPM in a certain biological condition as not expressed (NE). If the lncRNA genes are tagged with NE in all biological conditions available, they are most likely unreliable lncRNA genes. Of course, it is possible that this definition may change when novel biological conditions are covered.

2.5 Estimation of lncRNA expression capacity

All expressed genes(lncRNAs and mRNAs) are ranked in a specific condition (time point/stage/tissue/cell/component/processing). Specifically, genes with expression values greater than the upper quantile are classified as “H” (high expression level), those less than the lower quantile as “L” (low expression level), and the remaining as “M” (medium expression level). High-capacity lncRNAs (HCL) are genes with “H” classification in at least one condition, and low-capacity lncRNAs (LCL) are those with “L” in all conditions, and the remaining are medium-capacity lncRNAs (MCL). It is noted that with more biological conditions covered, LCL or MCL may change to MCL or HCL.

2.6 Identification of high-confidence featured lncRNAs

LncExpDB identifies and characterizes featured lncRNA genes that are specifically expressed in a certain cell line/tissue, differentially expressed in the context of cancer or virus infection, enriched in a subcellular compartment, dynamically expressed during cell differentiation or embryo/organ development, or periodically expressed with circadian rhythm.

The featured genes are identified using specialized methods with strict criteria:

Time-course expression patterns: R-square >= 0.7 and adjusted p-value < 0.05, maSigPro;

Stage-specific genes and tissue/cell-specific genes: τ (tissue-specific index) >= 0.9, maximum TPM >= 10;

Consistently expressed genes: τ <= 0.35, maximum TPM >= 10;

Differentially expressed genes in virus infection ,exosomes,cancer immunotherapy,human aging and Metabolic Diseases: |log2 foldchange| >= 1 and adjusted p-value <= 0.05, DeSeq2;

Organelle-enriched genes: log2 foldchange >= 1 and adjusted p-value <= 0.05, DeSeq2;

Circadian genes: meta2d and BH < 0.05, MetaCycle.

2.7 LncRNA-mRNA interaction prediction

LncExpDB predicts lncRNA-mRNA interactions based on co-expression networks. Co-expressions relationships between lncRNAs and mRNAs are identified using the Pearson correlation coefficient (adjusted p-value < 0.01 and |r|>=0.5). It is noted due to the extremely small sampling size (n = 4), the dataset of “COVID patients vs. normal control” is not analyzed in this section.

Database Usage

3.1 Quick start in LncExpDB

Enter a gene symbol or gene ID (LncExpDB ID) in the search box on the homepage to explore the lncRNA of interest. In the “Resources” part or “Context” section in the navigation bar, the click of each context will lead you to explore the expression profiles of featured lncRNAs and lncRNA-mRNA interactions across different biological conditions in the corresponding biological contexts, where you can view the defined featured genes or explore a group of lncRNA genes of interest with customized filtration.

To overview expression capacities/featured genes/interactions across different contexts, please click on “Expression Capacity”, “Featured Genes” and “Interactions” in the navigation bar.

3.2 Browse lncRNA genes in LncExpDB

You can browse all lncRNAs in the "Genes" page with the basic information of gene id/symbol, classification, chromosome, strand, location, gene length and transcript number. You can search lncRNAs of interest by gene id/transcript id derived from LncBook v1.2, RefLnc, NONCODE v5, GENCODE v33, CHESS v2.2, FANTOM-CAT (lv4_strigent) and BIGTranscriptome or gene symbol derived from HGNC, chromosome or classification type, and the gene id is linked to detailed information page of expression profiles in different contexts. In the detaied gene page, all corresponding gene and transcript id provide hyperlinks to their orginal pages. In addition, users can view our reference gene track on UCSC Genome Browser.

3.3 Explore featured genes in LncExpDB

You can explore featured lncRNAs in the "Featured Genes" page, which covers tens of thousands of featured genes with specific expression patterns in at least one biological context. You can filter and/or re-order the table content using the categories and search boxes in the header line. Each gene id is linked to detailed information page of expression profiles in different contexts.

3.4 View featured lncRNAs and interactions among biological contexts in LncExpDB

You can view all types of biological samples in the "Contexts" page including normal tissues and cell lines, organ development, preimplantation embryos, cell differentiation, subcellular localization, exosome, cancer cell line, virus infection and circadian rhythm. Each context page contains the tabs of “Featured Genes” and “Interaction”.

By clicking the tab of “Featured Genes”, you can select specific datasets of interest and browse all defined featured genes, e.g., specifically or consistently expressed genes in a certain context. In addition, you can select a specific group of genes with custom thresholds. You can filter and/or re-order the expression profile table using the categories and search boxes in the header line.

By clicking the tab of “Interactions”, you can select specific datasets of interest and browse the cis or trans interactions between lncRNAs and mRNAs. Moreover, you can select a specific group of interaction by custom thresholds or search the related interactions by lncRNA/protein-coding id or symbol.

3.5 Browse expression capacity in LncExpDB

In the "Expression Capacity" page, you can browse the lncRNA’s expression capacity in various biological contexts. You can filter for high-capacity lncRNAs in one or multiple contexts using the categories and in the header line of expression capacity table. Furthermore, the “Chart” enables visualization of expression level distribution among all the biological conditions. Each gene id is linked to detailed information page of expression profiles in different contexts.

3.6 Visualize lncRNA-mRNA interactions in LncExpDB

You can visualize all lncRNA-mRNA interactions in the “Interactions” page, which includes the detail information of lncRNAs-mRNA pairs, pearson correlation coefficient value, p values and distance. The “search by” tab allows you to narrow down the results according to gene of your interest. Each gene id is linked to detailed information page of expression profiles in different contexts.

3.7 Download data in LncExpDB

The “Downloads” page contains all the files that you can download such as: i) reference gene model for RNA-seq analysis, ii) expression profiles, iii) expression levels, iv) featured genes and v) co-expression matrix in various biological contexts.

3.8 Statistic results in LncExpDB

In the page of “Statistics”, you can find and download all statistical analytics results for i) gene annotation statistics, such as lncRNA integration, exon and transcript number distribution and lncRNA classification, ii) expression statistics, including expression profiles and distribution of featured lncRNAs in different biological contexts, and iii) lncRNA-mRNA interaction distribution.

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