功能与整合基因组学致力于基因组及其功能的大规模研究，包括生物过程的系统分析。该杂志将为研究界提供一个综合平台，研究人员可以在此分享、审查和讨论他们在重要生物学问题上的发现，最终使我们能够回答基本问题：基因组如何工作？

Functional and Integrative Genomics focuses on large-scale studies of genomes and their functions, including systematic analyses of biological processes. This journal provides a comprehensive platform for the research community, allowing researchers to share, review, and discuss their findings on significant biological issues, ultimately enabling us to address a fundamental question: How does the genome work?

《Functional and Integrative Genomics》致力于基因组及其功能的大规模研究，包括生物过程的系统分析。该杂志为研究界提供了一个综合平台，研究人员可以在此分享、审查和讨论他们在重要生物学问题上的发现，最终帮助我们回答一个基本问题：基因组是如何工作的？

Functional and Integrative Genomics

Kasmika Borah

Himanish Shekhar Das

Soumita Seth

Koushik Mallick

Zubair Rahaman

Saurav Mallik

Functional & Integrative Genomics

A review on advancements in feature selection and feature extraction for high-dimensional NGS data analysis

高维NGS数据分析中的特征选择与特征提取进展综述

Dirigent proteins (DIRs) are a new class of proteins that were identified during the 8-8' lignan biosynthetic pathway and involves the formation of ( +) or ( -)-pinoresinol through stereoselective coupling from E-coniferyl alcohol. These proteins are known to play a vital role in the development and stress response in plants. Various studies have reported the functional and structural characterization of dirigent gene family in different plants using in silico approaches. Here, we have summarized the importance of dirigent proteins in plants and their role in plant stress tolerance by analyzing the genome-wide analysis including gene structure, mapping of chromosomes, phylogenetic evolution, conserved motifs, gene structure, and gene duplications in important plants. Overall, this review would help to compare and clarify the molecular and evolutionary characteristics of dirigent gene family in different plants.

Preedhi Kapoor

Gurseen Rakhra

Vineet Kumar

Ridhi Joshi

Mahiti Gupta

Gurmeen Rakhra

Functional & integrative genomics

Funct Integr Genomics

Insights into the functional characterization of DIR proteins through genome-wide in silico and evolutionary studies: a systematic review.

We report the construction and characterization of the first soybean yeast artificial chromosome (YAC) library using high-molecular weight DNA isolated from leaf nuclei of the cultivar Conrad 94 that carries Phytophthora resistance genes Rps1-k and Rps6. The quality of this library has been evaluated through analysis of 393 randomly selected YAC clones. The library consists of 36864 clones, of which approximately 19956 carry single soybean YACs with an average size of about 285 kb. The library represents approximately five soybean genome equivalents. The probability of finding any soybean sequences from this library is about 0.99. The library was screened for 43 SSR markers representing the whole soybean genome. We were able to identify positive YAC pools for 95% of the SSR markers. Two YAC clones carrying molecular markers linked to the Rps6 gene were identified. The YAC library reported here would be a useful resource for map-based cloning of agronomically important soybean genes and also to complement the effort towards construction of the physical map for the soybean genome.

Dipak K Santra

Devinder Sandhu

Thomas Tai

Madan K Bhattacharyya

Construction and characterization of a soybean yeast artificial chromosome library and identification of clones for the Rps6 region.

Soybean is an economically important leguminous crop, and pod dehiscence of soybean could cause huge yield loss. In this study, we measured fruit-cracking forces and percentages of dehisced pods for ten soybean accessions, then separated them into two groups as shattering-sensitive (SS) and shattering-resistant (SR) soybeans. Pod transcriptomes from these two groups were analyzed, and 225 differentially expressed genes (DEGs) were identified between SS and SR soybeans. Some of these DEGs have been previously reported to be associated with pod dehiscence in soybean. The expression patterns of selected DEGs were validated by real-time quantitative reverse transcription PCR, which confirmed the expression changes found in RNA-seq analysis. We also de novo identified 246 soybean pod-long intergenic ncRNAs (lincRNAs), 401 intronic lncRNAs, and 23 antisense lncRNAs from these transcriptomes. Furthermore, genes and lincRNAs co-expression network analysis showed that there are distinct expression patterns between SS and SR soybeans in some co-expression modules. In conclusion, we systematically investigated potential genes and molecular pathways as candidates for differences in soybean pod dehiscence and will provide a useful resource for molecular breeding of soybeans.

Xiang Kang

Jingjing Cai

Yexin Chen

Yuchuan Yan

Songtao Yang

Reqing He

Dong Wang

Youlin Zhu

Pod-shattering characteristics differences between two groups of soybeans are associated with specific changes in gene expression.

Colorectal cancer is a malignant tumor of the digestive system originating from abnormal cell proliferation in the colon or rectum, often leading to gastrointestinal symptoms and severe health issues. Nucleotide metabolism, which encompasses the synthesis of DNA and RNA, is a pivotal cellular biochemical process that significantly impacts both the progression and therapeutic strategies of colorectal cancer
For single-cell RNA sequencing (scRNA-seq), five functions were employed to calculate scores related to nucleotide metabolism. Cell developmental trajectory analysis and intercellular interaction analysis were utilized to explore the metabolic characteristics and communication patterns of different epithelial cells. These findings were further validated using spatial transcriptome RNA sequencing (stRNA-seq). A risk model was constructed using expression profile data from TCGA and GEO cohorts to optimize clinical decision-making. Key nucleotide metabolism-related genes (NMRGs) were functionally validated by further in vitro experiments.
In both scRNA-seq and stRNA-seq, colorectal cancer (CRC) exhibited unique cellular heterogeneity, with myeloid cells and epithelial cells in tumor samples displaying higher nucleotide metabolism scores. Analysis of intercellular communication revealed enhanced signaling pathways and ligand-receptor interactions between epithelial cells with high nucleotide metabolism and fibroblasts. Spatial transcriptome sequencing confirmed elevated nucleotide metabolism states in the core region of tumor tissue. After identifying differentially expressed NMRGs in epithelial cells, a risk prognostic model based on four genes effectively predicted overall survival and immunotherapy outcomes in patients. High-risk group patients exhibited an immunosuppressive microenvironment and relatively poorer prognosis and responses to chemotherapy and immunotherapy. Finally, based on data analysis and a series of cellular functional experiments, ACOX1 and CPT2 were identified as novel therapeutic targets for CRC.
In this study, a comprehensive analysis of NMRGs in CRC was conducted using a combination of single-cell sequencing, spatial transcriptome sequencing, and high-throughput data. The prognostic model constructed with NMRGs shows potential as a standalone prognostic marker for colorectal cancer patients and may significantly influence the development of personalized treatment approaches for CRC.

Songyun Zhao

Pengpeng Zhang

Sen Niu

Jiaheng Xie

Yuankun Liu

Yuan Liu

Ning Zhao

Chao Cheng

Peihua Lu

Functional &amp; Integrative Genomics

Targeting nucleotide metabolic pathways in colorectal cancer by integrating scRNA-seq, spatial transcriptome, and bulk RNA-seq data

整合单细胞RNA测序、空间转录组和批量RNA测序数据靶向结直肠癌的核苷酸代谢途径

Lung adenocarcinoma (LUAD) is one of the deadliest cancers. Epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI)-targeted therapy is an important approach for treating LUAD. However, the development of acquired resistance poses a serious clinical challenge. Our objective was to explore the differentially expressed genes (DEGs) associated with EGFR and detect biomarkers for diagnosing and treating osimertinib resistance in LUAD patients. LUAD datasets were downloaded from public databases. Differential expression analysis was performed to screen DEGs, and prognostic modules were constructed by Cox regression. Enrichment analysis, gene regulatory network analysis and immune microenvironment analysis were employed to explore the underlying mechanisms in LUAD. Finally, the expression of prognosis module genes (PMGs) was validated in 8 LUAD tissue specimens and 5 cell lines by qRT-PCR. In total, 13 differential module genes (BIRC3, CCT6A, CPLX2, GLCCI1, GSTA1, HLA-DQB2, ID1, KCTD12, MUC15, NOTUM, NT5E, TCIM, and TM4SF4) were screened for the construction of a prognostic module. Notably, CCT6A and KCTD12 demonstrated excellent accuracy in the diagnosis of LUAD. Immune dysregulation and BIRC3, HLA-DQB2, KCTD12, and NT5E expression were significantly associated with invasive immune cells in LUAD patients. The expression level of CCT6A was highest in PC9-OR and H1975-OR cells, while the expression level of KCTD12 was highest in paracancerous tissue and HBE cells. The constructed prognostic model showed promise in predicting the survival of LUAD patients. Notably, KCTD12 and CCT6A might be candidate biomarkers for improving diagnostic performance and guiding individualized therapy for EGFR-TKI-resistant LUAD patients.

Haiwen Li

Li Yang

Quan Yang

Zhu Liang

Wenmei Su

Lili Yu

Integration of osimertinib-targeted EGFR gene-associated differential gene expression in constructing a prognostic model for lung adenocarcinoma

奥希替尼靶向EGFR基因相关差异基因表达在构建肺腺癌预后模型中的整合

Kaouthar Feki

Sana Tounsi

Hanen Kamoun

Abdulrahman Al-Hashimi

Faiçal Brini

Correction to: Decoding the role of durum wheat ascorbate peroxidase TdAPX7B-2 in abiotic stress response

更正：解码杜兰小麦抗坏血酸过氧化物酶TdAPX7B-2在非生物胁迫响应中的作用

Metastasis is responsible for approximately 90% of lethality from solid tumors. Metabolic abnormalities are one of the key characteristics of tumor cells, closely associated with tumorigenesis and progression. The de novo synthesis pathway of serine is a key metabolic bypass in glycolysis, which could provide material and energy basis for the rapid proliferation of tumor cells by mediating one-carbon metabolism. The transformation of metabolic patterns is particularly pronounced in HCC, often leading to a high dependence of HCC cells on glycolysis. However, up to now, the underlying relationship between serine metabolism and HCC metastasis remains largely unknown. Through a series of bioinformatics methods, we reported CCT6A, a serine related gene, was particularly associated with metastatic events of HCC. We furtherly demonstrated that CCT6A was highly expressed in HCC cells with high metastatic potential. Gain- and loss-of-function analyses showed that CCT6A could promote HCC cells migration and invasion. Mechanistically, CCT6A was found to be interacted with RPS3, and might potentiate the metastasis of HCC by affecting some metabolic processes. Totally, our results suggest that the metabolic reprogramming induced by interacting between CCT6A and RPS3 could advance HCC metastasis, making the CCT6A/RPS3 axis a promising target for therapeutic intervention.

Hongwei Cui

Li Jiang

Yujiao Zhou

You Zhou

Fan Li

Zhenzhen Zhang

Serine related gene CCT6A promotes metastasis of hepatocellular carcinoma via interacting with RPS3

丝氨酸相关基因CCT6A通过与RPS3相互作用促进肝细胞癌转移

Pathways-based clustering methods have been proposed to explore tumor heterogeneity. However, such methods are currently disadvantageous in that specific pathways need to be explicitly claimed. We developed the PathClustNet algorithm, a pathway-based clustering method designed to identify cancer subtypes. This method first detects gene clusters and identifies overrepresented pathways associated with them. Based on the pathway enrichment scores, it reveals cancer subtypes by clustering analysis. We applied the method to TCGA pan-cancer data and identified four pan-cancer subtypes, termed C1, C2, C3 and C4. C1 exhibited high metabolic activity, favorable survival, and the lowest TP53 mutation rate. C2 had high immune, developmental, and stromal pathway activities, the lowest tumor purity, and intratumor heterogeneity. C3, which overexpressed cell cycle and DNA repair pathways, was the most genomically unstable and had the highest TP53 mutation rate. C4 overrepresented neuronal pathways, with the lowest response rate to chemotherapy, but the highest tumor purity and genomic stability. Furthermore, age showed positive correlations with most pathways but a negative correlation with neuronal pathways. Smoking, viral infections, and alcohol use were found to affect the activities of neuron, cell cycle, immune, stromal, developmental, and metabolic pathway in varying degrees. The PathClustNet algorithm unveils a novel classification of pan-cancer based on metabolic, immune, stromal, developmental, cell cycle, and neuronal pathways. These subtypes display different molecular and clinical features to warrant the investigation of precision oncology.

Mengli Xu

Hongjing Ai

Danni Wang

Xiaosheng Wang

Gene clusters-based pathway enrichment analysis identifies four pan-cancer subtypes with distinct molecular and clinical features

基于基因簇的通路富集分析识别出四种具有不同分子和临床特征的泛癌亚型

APX proteins are H2O2-scavenging enzymes induced during oxidative stress. In the first part of this study, we provided an extensive knowledge on the APX family of Triticum durum, TdAPX and their related TdAPX-R, via the genome wide analysis. The outcomes showed that these proteins are clustered into four major subgroups. Furthermore, the exon-intron structure and the synteny analyses revealed that during evolution the genes TdAPX and TdAPX-R are relatively conserved. Besides, during their evolution, these genes underwent purifying selection pressure and were duplicated in segmental. In parallel, the analysis of the conserved motifs and the multiple sequence alignment demonstrated that the residues involved in the active sites, heme- and cations-binding are conserved only in TdAPX proteins. Following the RNA-seq data and the regulatory elements analyses, we focused in the second part of this study on the functional characterization of TdAPX7B-2. The qRT-PCR data showed the upregulation of TdAPX7B-2 essentially in leaves of durum wheat exposed to salt, cold, drought, metals and ABA treatments. The tolerance phenotype of the TdAPX7B-2-expressing Arabidopsis lines to salt, direct-induced oxidative stress and heavy metals was manifested by the development of root system, proline accumulation and induction of the antioxidant CAT, SOD and POD enzymes to maintain the non-toxic H2O2 levels. Likewise, the response to salt stress and direct-oxidative stress of the transgenic lines was accompanied mainly by the induction of AtNCED3, AtRD29A/B and AtERD1.

Abdulrahman Al-Hashim

Decoding the role of durum wheat ascorbate peroxidase TdAPX7B-2 in abiotic stress response

解码杜兰小麦抗坏血酸过氧化物酶TdAPX7B-2在非生物胁迫响应中的作用

Abbreviation	Funct Integr Genomics
Journal Impact	3.86
Quartiles(Global)	GENETICS & HEREDITY(Q1)

ISSN	1438-793X, 1438-7948
h-index	84

Publication Information	Publisher: Springer Nature，Publishing cycle: Bimonthly，Journal Type: journal，Open Access Journals: No
Basic data	Year of publication: 2000，Proportion of original research papers: 94.38%，Self Citation Rate:38.50%， Gold OA Rate: 12.90%
Average review cycle	网友分享经验：平均3.0个月
Average recruitment ratio	网友分享经验：约50%

Functional and Integrative Genomics

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