TFTG: A comprehensive database for human transcription factors and their targets.

Transcription factors (TFs) are major contributors to gene transcription, especially in controlling cell-specific gene expression and disease occurrence and development. Uncovering the relationship between TFs and their target genes is critical to understanding the mechanism of action of TFs. With the development of high-throughput sequencing techniques, a large amount of TF-related data has accumulated, which can be used to identify their target genes. In this study, we developed TFTG (Transcription Factor and Target Genes) database (http://tf.liclab.net/TFTG), which aimed to provide a large number of available human TF-target gene resources by multiple strategies, besides performing a comprehensive functional and epigenetic annotations and regulatory analyses of TFs. We identified extensive available TF-target genes by collecting and processing TF-associated ChIP-seq datasets, perturbation RNA-seq datasets and motifs. We also obtained experimentally confirmed relationships between TF and target genes from available resources. Overall, the target genes of TFs were obtained through integrating the relevant data of various TFs as well as fourteen identification strategies. Meanwhile, TFTG was embedded with user-friendly search, analysis, browsing, downloading and visualization functions. TFTG is designed to be a convenient resource for exploring human TF-target gene regulations, which will be useful for most users in the TF and gene expression regulation research.

Micelles Cascade Assembly to Tandem Porous Catalyst for Waste Plastics Upcycling.

Catalytic upcycling of polyolefins into high-value chemicals represents the direction in end-of-life plastics valorization, but poses great challenges. Here, we report the synthesis of a tandem porous catalyst via a micelle cascade assembly strategy for selectively catalytic cracking of polyethylene into olefins at a low temperature. A hierarchically porous silica layer from mesopore to macropore is constructed on the surface of microporous ZSM-5 nanosheets through cascade assembly of dynamic micelles. The outer macropore arrays can adsorb bulky polyolefins quickly by the capillary and hydrophobic effects, enhancing the diffusion and access to active sites. The middle mesopores present a nanoconfinement space, pre-cracking polyolefins into intermediates by weak acid sites, which then transport into zeolites micropores for further cracking by strong Brønsted acid sites. The hierarchically porous and acidic structures, mimicking biomimetic protease catalytic clefts, ideally match the tandem cracking steps of polyolefins, thus suppressing coke formation and facilitating product escape. As a result, light hydrocarbons (C1-C7) are produced with a yield of 443 mmol·gZSM-5-1, where 74.3% of them are C3-C6 olefins, much superior to ZSM-5 and porous silica catalysts. This tandem porous catalyst exemplifies a superstructure design of catalytic cracking catalysts for industrial and economical upcycling of plastic wastes.

scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species.

Chromatin accessibility profiles at single cell resolution can reveal cell type-specific regulatory programs, help dissect highly specialized cell functions and trace cell origin and evolution. Accurate cell type assignment is critical for effectively gaining biological and pathological insights, but is difficult in scATAC-seq. Hence, by extensively reviewing the literature, we designed scATAC-Ref (https://bio.liclab.net/scATAC-Ref/), a manually curated scATAC-seq database aimed at providing a comprehensive, high-quality source of chromatin accessibility profiles with known cell labels across broad cell types. Currently, scATAC-Ref comprises 1 694 372 cells with known cell labels, across various biological conditions, >400 cell/tissue types and five species. We used uniform system environment and software parameters to perform comprehensive downstream analysis on these chromatin accessibility profiles with known labels, including gene activity score, TF enrichment score, differential chromatin accessibility regions, pathway/GO term enrichment analysis and co-accessibility interactions. The scATAC-Ref also provided a user-friendly interface to query, browse and visualize cell types of interest, thereby providing a valuable resource for exploring epigenetic regulation in different tissues and cell types.

SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse.

Super-enhancers (SEs) play an essential regulatory role in various biological processes and diseases through their specific interaction with transcription factors (TFs). Here, we present the release of SEanalysis 2.0 (http://licpathway.net/SEanalysis), an updated version of the SEanalysis web server for the comprehensive analyses of transcriptional regulatory networks formed by SEs, pathways, TFs, and genes. The current version added mouse SEs and further expanded the scale of human SEs, documenting 1 167 518 human SEs from 1739 samples and 550 226 mouse SEs from 931 samples. The SE-related samples in SEanalysis 2.0 were more than five times that in version 1.0, which significantly improved the ability of original SE-related network analyses ('pathway downstream analysis', 'upstream regulatory analysis' and 'genomic region annotation') for understanding context-specific gene regulation. Furthermore, we designed two novel analysis models, 'TF regulatory analysis' and 'Sample comparative analysis' for supporting more comprehensive analyses of SE regulatory networks driven by TFs. Further, the risk SNPs were annotated to the SE regions to provide potential SE-related disease/trait information. Hence, we believe that SEanalysis 2.0 has significantly expanded the data and analytical capabilities of SEs, which helps researchers in an in-depth understanding of the regulatory mechanisms of SEs.

Analysis of the differential expression and prognostic relationship of DEGs in AML based on TCGA database.

BACKGROUND: Acute myeloid leukemia (AML) is a common and lethal hematological malignant hyperplastic disease originating from hematopoietic stem cells. The purpose of this study is to obtain the key differentially expressed gene (DEG) related to the survival of AML by The Cancer Genome Atlas (TCGA) database and to verify these genes by a clinical follow-up investigation, in order to identify valuable predictive and prognostic biomarkers for early diagnosis of AML and predict the survival rates. METHODS: The RNA sequencing (RNA-Seq) data and clinical information of TCGA-LAML were downloaded from the TCGA database. After that we (1) screened the survival-related DEGs by Cox regression analysis, (2) selected the cytogenetics risk-related DEGs by DESeq2 R package, and (3) filtrated the genes in the top10 pathways of up-regulated and down-regulated of Normalization Enrichment Score (NES) by Gene Set Enrichment Analysis (GSEA). Finally, we focused the intersectional genes of above three parts as the key gene of the present study. The following Multivariate.

CanMethdb: a database for genome-wide DNA methylation annotation in cancers.

MOTIVATION: DNA methylation within gene body and promoters in cancer cells is well documented. An increasing number of studies showed that cytosine-phosphate-guanine (CpG) sites falling within other regulatory elements could also regulate target gene activation, mainly by affecting transcription factors (TFs) binding in human cancers. This led to the urgent need for comprehensively and effectively collecting distinct cis-regulatory elements and TF-binding sites (TFBS) to annotate DNA methylation regulation. RESULTS: We developed a database (CanMethdb, http://meth.liclab.net/CanMethdb/) that focused on the upstream and downstream annotations for CpG-genes in cancers. This included upstream cis-regulatory elements, especially those involving distal regions to genes, and TFBS annotations for the CpGs and downstream functional annotations for the target genes, computed through integrating abundant DNA methylation and gene expression profiles in diverse cancers. Users could inquire CpG-target gene pairs for a cancer type through inputting a genomic region, a CpG, a gene name, or select hypo/hypermethylated CpG sets. The current version of CanMethdb documented a total of 38 986 060 CpG-target gene pairs (with 6 769 130 unique pairs), involving 385 217 CpGs and 18 044 target genes, abundant cis-regulatory elements and TFs for 33 TCGA cancer types. CanMethdb might help biologists perform in-depth studies of target gene regulations based on DNA methylations in cancer. AVAILABILITY AND IMPLEMENTATION: The main program is available at https://github.com/chunquanlipathway/CanMethdb. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Impact of engineering renovation on dynamic health risk assessment of mercury in a thermometer enterprise.

The occupational health risk assessments (OHRA) of inorganic mercury (Hg) are rarely reported. We conducted an internal and external exposure monitoring of employees in a thermometer enterprise which experienced the renovation of occupational health engineering, followed by an evaluation on the health risks of Hg exposure with four OHRA methods in order to find out a most suitable model. The results showed that the concentrations of airborne and urinary Hg in all testing positions and subjects obviously decreased after the engineering renovation, meeting the occupational exposure limits (OELs) of China. Subsequently, four OHRA models, namely the models from US Environmental Protection Agency (EPA), Ministry of Manpower (MOM), International Council on Mining and Metals (ICMM), and Classification of occupational hazards at workplaces Part 2: Occupational exposure to chemicals (GBZ/T 229.2-2010) were applied in the qualitative risk assessment. And the evaluation results of different methods were standardized by risk ratio (RR), which indicated MOM, ICMM risk rating, and GBZ/T 229.2 models were consistent with the order of inherent risk levels in those working processes. The order of RR between four models was: RR EPA > RR ICMM > RR MOM> RR GBZ/T229.2 (P < 0.05). Based on the strict limits of Hg, GBZ/T 229.2, and MOM methods may have more potentials in practical application. Though the working environment has been significantly improved via engineering renovation, it is strongly suggested that the thermometer company conduct more effective risk management covering all production processes to minimize Hg exposure levels and health risk ratings.

GREAP: a comprehensive enrichment analysis software for human genomic regions.

The rapid development of genomic high-throughput sequencing has identified a large number of DNA regulatory elements with abundant epigenetics markers, which promotes the rapid accumulation of functional genomic region data. The comprehensively understanding and research of human functional genomic regions is still a relatively urgent work at present. However, the existing analysis tools lack extensive annotation and enrichment analytical abilities for these regions. Here, we designed a novel software, Genomic Region sets Enrichment Analysis Platform (GREAP), which provides comprehensive region annotation and enrichment analysis capabilities. Currently, GREAP supports 85 370 genomic region reference sets, which cover 634 681 107 regions across 11 different data types, including super enhancers, transcription factors, accessible chromatins, etc. GREAP provides widespread annotation and enrichment analysis of genomic regions. To reflect the significance of enrichment analysis, we used the hypergeometric test and also provided a Locus Overlap Analysis. In summary, GREAP is a powerful platform that provides many types of genomic region sets for users and supports genomic region annotations and enrichment analyses. In addition, we developed a customizable genome browser containing >400 000 000 customizable tracks for visualization. The platform is freely available at http://www.liclab.net/Greap/view/index.

CATA: a comprehensive chromatin accessibility database for cancer.

Accessible chromatin refers to the active regions of a chromosome that are bound by many transcription factors (TFs). Changes in chromatin accessibility play a critical role in tumorigenesis. With the emergence of novel methods like Assay for Transposase-accessible Chromatin Sequencing, a sequencing method that maps chromatin-accessible regions (CARs) and enables the computational analysis of TF binding at chromatin-accessible sites, the regulatory landscape in cancer can be dissected. Herein, we developed a comprehensive cancer chromatin accessibility database named CATA, which aims to provide available resources of cancer CARs and to annotate their potential roles in the regulation of genes in a cancer type-specific manner. In this version, CATA stores 2 991 163 CARs from 23 cancer types, binding information of 1398 TFs within the CARs, and provides multiple annotations about these regions, including common single nucleotide polymorphisms (SNPs), risk SNPs, copy number variation, somatic mutations, motif changes, expression quantitative trait loci, methylation and CRISPR/Cas9 target loci. Moreover, CATA supports cancer survival analysis of the CAR-associated genes and provides detailed clinical information of the tumor samples. Database URL: CATA is available at http://www.xiejjlab.bio/cata/.

The Effect of HER2 Single Nucleotide Polymorphisms on Cervical Cancer Susceptibility and Survival in a Chinese Population.

Background: Cervical cancer (CCa) is a multifactorial gynecologic disease worldwide. Effects of HER2 polymorphisms, especially those in exonic region, have been investigated in many gynecologic diseases. In this study, we evaluated the influence of functional HER2 polymorphisms on susceptibility and survival of CCa in a Chinese population. Methods: We genotyped the HER2 exonic polymorphisms by TaqMan in both case-control study (413 CCa patients vs. 396 controls) and survival study (413 CCa patients). Logistic regression and Cox regression were adopted to evaluate the genetic association with the risk and outcomes of CCa, respectively. Results: In the case-control study, there was no significant difference between patients and controls in either HER2 rs1136201 or rs1058808. However, when combined, these two polymorphisms demonstrated a significant hazardous effect for CCa (P = 0.012). Besides, number of variants was also influential (P trend =0.002). In survival analysis, dominant model of rs1136201 and co-dominant modelof rs1058808 were significantly associated with the survival (P = 0.037 and P =0.028). The combination of rs1136201 and rs1058808 also negatively impacted CCa survival (P = 0.009). Cox regression further revealed the significance of the polymorphism combination (ß = 0.38, P = 0.025, HR= 1.47, 95%CI = 1.05-2.05). Functional assay of these polymorphisms demonstrated that rs1058808 G allele was associated with stronger expression of HER2 gene. Conclusions: Our results suggested that the combination of HER2 rs1136201and rs1058808 was significantly associated with the susceptibility of CCa. Besides, this combination of polymorphism s also substantially impacted the survival of CCa patients.

Association between single nucleotide polymorphism (rs4252424) in TRPV5 calcium channel gene and lead poisoning in Chinese workers.

BACKGROUND: Lead (Pb) is broadly used in various industries and causes irreversible damage to human tissues, organs, and systems. Studies have revealed that lead exerts toxic effects via interfering with calcium channel. METHODS: In the present study, we investigated whether single nucleotide polymorphisms (SNPs) in TRPV5, a calcium channel-related gene, were associated with lead exposure susceptibility. By using TaqMan SNP genotyping, we performed genotyping of eight TRPV5 tag-SNPs in 1,130 lead-exposed Chinese workers with similar lead exposure level. RESULTS: Single nucleotide polymorphism rs4252424 was significantly associated with lead susceptibility, measured by blood lead level (BLL) (ß = -0.069, plinear  = 0.029). However, there was no significant association between any other seven SNPs and BLL. The further expression Quantitative Trait Loci displayed that CC genotype of rs4252424 is significant associated with higher BLL than CT (p < 0.0001). CONCLUSION: We conclude that SNP rs4252424 has the potential to evaluate lead susceptibility in the Chinese occupational population, and further enhance lead exposure prevention and intervention.

Identification of differential plasma miRNA profiles in Chinese workers with occupational lead exposure.

Elevated lead absorptions are hazardous factors in lead-related workers. Previous studies have found its toxic impacts on nervous, circulatory, and metabolic systems. We hypothesized that alteration of miRNAs profile in plasma was closely associated with lead exposure. We analyzed to identify lead-related miRNAs in workers occupationally exposed to lead. Microarray assay was performed to detect plasma miRNA between workers with high and minimal lead exposure in the discovery stage. The following prediction of miRNAs' candidate target genes was carried out by using miRecords, STRING, and KEGG databases. We finally identified four miRNAs significantly associated with high level of blood lead. miR-520c-3p (*P=0.014), miR-211 (*P=0.019), and miR-148a (*P=0.031) were downexpressed in workers with high lead exposure and with high blood lead level (BLL), while miR-572(*P=0.027) displayed an opposite profile. Functional analysis of miRNAs displayed that these miRNAs could trigger different cellular genes and pathways. People under chronic lead exposure had a diverse 'fingerprint' plasma miRNA profile. Our study suggested that miR-520c-3p, miR-211, miR-148a, and miR-572 were the potential biomarkers for lead susceptibility in Chinese.