DOI: 10.57760/sciencedb.o00019.00014
title: Expression data and gene orthogroup results for manuscript "Gene regulation sheds on the rise and evolution of spider venom gland"
title: Expression data and gene orthogroup results for manuscript "Gene regulation sheds on the rise and evolution of spider venom gland"

description: We compared the genome and transcriptome data from various lineages by integrating gene expression analyses, coding gene comparison and gene selection analyses across spiders, tick, mite, and insects. This dataset includes six matrices for manuscript "Gene regulation sheds on the rise and evolution of spider venom gland".The detailed introduction of matrices are listed below:1.FPKM_Matrix_of_Orthologs_among_all_taxa_based_on_52_RNA_samples.txt:We obtained ortholog expression matrix which had high-confidence alignments across the multiple taxa based on the 1,716 one-to-one orthologs. We calculated gene expression values by mapping all of the RNA reads from 52 samples back to the trimmed orthologs of each species using RSEM software. A gene expression matrix with 52 columns, each representing a sample, and 1,716 lines, each corresponding to the expression of an ortholog, was constructed.2.Raw_Read_Counts_of_17_RNA_Samples_in_Fruit_Fly.txt:A total of 17 RNA-seq samples were used to obtain the significantly up-regulated gene clusters of salivary gland in fruit fly, by comparing with the different tissue transcriptomes, such as ovary, brain, and heart. The raw read counts of each gene were provided.3.Raw_Read_Counts_of_15_RNA_Samples_in_House_Spider.txt:A total of 15 RNA-seq samples were used to obtain the significantly up-regulated gene clusters of venom glands in house spider, by comparing with the different tissue transcriptomes, such as ovary, brain, and silk glands. The raw read counts of each gene were provided.4.WGCNA&FPKM_of_22_salivary_glands_Fruit_Fly.xlsx:A total of 22 salivary gland RNA-seq samples were aligned to the genome of fruit fly (GCA_000001215.4) using HISAT2 program. We counted read counts per gene through HTSeq framework. Gene counts were then normalized among samples using the FPKM normalization method. We used R package WGCNA to perform Gene Co-Expression Network Analysis. FPKM matrix and result of WGCNA are provided.5.WGCNA&FPKM_of_22_ovary_Fruit_Fly.xlsx:A total of 22 ovary RNA-seq samples of fruit fly were used. The methods of mapping and normalization are same as above.6.Orthogroup_of_11_Species_from_Orthofinder_Program.xlsx:Gene families of 11 species across arthropods were inferred with Orthofinder program. Two matrices of gene counts and gene id for each gene orthogroup were provided.
description: We compared the genome and transcriptome data from various lineages by integrating gene expression analyses, coding gene comparison and gene selection analyses across spiders, tick, mite, and insects. This dataset includes six matrices for manuscript "Gene regulation sheds on the rise and evolution of spider venom gland".The detailed introduction of matrices are listed below:1.FPKM_Matrix_of_Orthologs_among_all_taxa_based_on_52_RNA_samples.txt:We obtained ortholog expression matrix which had high-confidence alignments across the multiple taxa based on the 1,716 one-to-one orthologs. We calculated gene expression values by mapping all of the RNA reads from 52 samples back to the trimmed orthologs of each species using RSEM software. A gene expression matrix with 52 columns, each representing a sample, and 1,716 lines, each corresponding to the expression of an ortholog, was constructed.2.Raw_Read_Counts_of_17_RNA_Samples_in_Fruit_Fly.txt:A total of 17 RNA-seq samples were used to obtain the significantly up-regulated gene clusters of salivary gland in fruit fly, by comparing with the different tissue transcriptomes, such as ovary, brain, and heart. The raw read counts of each gene were provided.3.Raw_Read_Counts_of_15_RNA_Samples_in_House_Spider.txt:A total of 15 RNA-seq samples were used to obtain the significantly up-regulated gene clusters of venom glands in house spider, by comparing with the different tissue transcriptomes, such as ovary, brain, and silk glands. The raw read counts of each gene were provided.4.WGCNA&FPKM_of_22_salivary_glands_Fruit_Fly.xlsx:A total of 22 salivary gland RNA-seq samples were aligned to the genome of fruit fly (GCA_000001215.4) using HISAT2 program. We counted read counts per gene through HTSeq framework. Gene counts were then normalized among samples using the FPKM normalization method. We used R package WGCNA to perform Gene Co-Expression Network Analysis. FPKM matrix and result of WGCNA are provided.5.WGCNA&FPKM_of_22_ovary_Fruit_Fly.xlsx:A total of 22 ovary RNA-seq samples of fruit fly were used. The methods of mapping and normalization are same as above.6.Orthogroup_of_11_Species_from_Orthofinder_Program.xlsx:Gene families of 11 species across arthropods were inferred with Orthofinder program. Two matrices of gene counts and gene id for each gene orthogroup were provided.