cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10679006
title: Raw 4D-STEM tilt-series data of T4-bacteriophages

description: 4D-STEM tilt-series (tom1 and tom2) acquired using the SavvyScan system with ARINA/DECTRIS pixelated detector. 

Microscope settings: F20 transmission electron microscope, 200KV, microprobe 30u, SS9, gun5, 1.5nm/pix scan.

SerialEM settings: 1024X1024 probe locations per tilt view, dose-symmetric with group of 3, direction minus to plus, steps of 2 deg (tom1) and 3 deg (tom2).

File format:   [name of series]_s[tilt view number]_data_[file number].h5
DOI: 10.6084/m9.figshare.8207513
title: MOESM4 of LncRNA H19 regulates PI3Kâ Akt signal pathway by functioning as a ceRNA and predicts poor prognosis in colorectal cancer: integrative analysis of dysregulated ncRNA-associated ceRNA network

description: Additional file 4. RNAs correlated with overall survival in the ceRNA network.
DOI: 10.6084/m9.figshare.8207531
title: Additional file 12: of Novel secretome-to-transcriptome integrated or secreto-transcriptomic approach to reveal liquid biopsy biomarkers for predicting individualized prognosis of breast cancer patients

description: Table S4. Basal GEOâ +â TCGAR2. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.12926073
title: Additional file 1 of A systematic study of critical miRNAs on cells proliferation and apoptosis by the shortest path

description: Additional file 1.
DOI: 10.6084/m9.figshare.12926073.v1
title: Additional file 1 of A systematic study of critical miRNAs on cells proliferation and apoptosis by the shortest path

description: Additional file 1.
DOI: 10.6084/m9.figshare.12926066.v1
title: Additional file 10 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 10: Table S9. The SNP loci associated with yield-related traits have been detected via GWAS method in upland cotton.
DOI: 10.6084/m9.figshare.12926084
title: Additional file 4 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 4: Table S3. Analysis of variance of three yield-related traits in four planting environments.
DOI: 10.6084/m9.figshare.21317550
title: Unigenes annotation of M. anguillicaudatus

description: Unigenes annotation of  loach
DOI: 10.6084/m9.figshare.15020639
title: Additional file 2 of Investigating causal relationships between exposome and human longevity: a Mendelian randomization analysis

description: Additional file 2: Table S13. Mendelian randomization results of all traits in primary analysis using dataset of 90th percentile longevity. Table S14. Mendelian randomization results of all traits in secondary analysis using dataset of 99th percentile longevity.
DOI: 10.6084/m9.figshare.8207555
title: Additional file 2: of High-resolution mapping of quantitative trait loci controlling main floral stalk length in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

description: Table S2. SNP markers and mutant genes between the confidence intervals identified in Chinese cabbage. (XLSX 736 kb)
DOI: 10.6084/m9.figshare.17120405.v1
title: Additional file 2 of Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data

description: Additional file 2. Conserved and rewired miRNA-mRNA regulatory networks and hub miRNAs.
DOI: 10.6084/m9.figshare.15020723
title: Additional file 1 of Analyzing the gonadal transcriptome of the frog Hoplobatrachus rugulosus to identify genes involved in sex development

description: Additional file 1.
DOI: 10.6084/m9.figshare.17120411.v1
title: Additional file 3 of Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data

description: Additional file 3. Conserved and rewired targets associated with miR-17/92 family.
DOI: 10.6084/m9.figshare.8207528.v1
title: Additional file 11: of Novel secretome-to-transcriptome integrated or secreto-transcriptomic approach to reveal liquid biopsy biomarkers for predicting individualized prognosis of breast cancer patients

description: Table S3. Luminal-Specific Secreted ProteinsR2. (XLSX 94 kb)
DOI: 10.6084/m9.figshare.8207495
title: MOESM1 of LncRNA H19 regulates PI3Kâ Akt signal pathway by functioning as a ceRNA and predicts poor prognosis in colorectal cancer: integrative analysis of dysregulated ncRNA-associated ceRNA network

description: Additional file 1. The differentially expressed mRNAs, lncRNAs, pseudogenes, and miRNA in CRC.
DOI: 10.6084/m9.figshare.12926087
title: Additional file 5 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 5: Table S4. The significant SNPLDB loci associated with BN, BW and LP, respectively.
DOI: 10.6084/m9.figshare.12926093
title: Additional file 7 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 7: Table S6. Gene names expressed mainly in fibers or ovules of upland cotton by two RNA-seq data.
DOI: 10.6084/m9.figshare.8207504.v1
title: MOESM3 of LncRNA H19 regulates PI3Kâ Akt signal pathway by functioning as a ceRNA and predicts poor prognosis in colorectal cancer: integrative analysis of dysregulated ncRNA-associated ceRNA network

description: Additional file 3. GO terms of differentially expressed mRNAs in the ceRNA network.
DOI: 10.6084/m9.figshare.12926099
title: Additional file 9 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 9: Table S8. The KEGG results of 16 potential candidate genes controlling target traits.
DOI: 10.1594/pangaea.908192
title: Strontium/Calcium, Iron/Calcium and Silicon/Calcium ratio of the Coccolith fraction from sediment core MD03-2699

description: This dataset from site MD03-2699, at the Iberian margin, contains depth, age and elemental rations of the Coccolith fraction (&lt; 20µm).
DOI: 10.6084/m9.figshare.7158980
title: supplementary material.csv

description: We have presented the parameters of every nanostructure (long axis and short axis) we design for the chromatic metalens as well as the achromatic counterpart in the supplementary material.
DOI: 10.6084/m9.figshare.8207513.v1
title: MOESM4 of LncRNA H19 regulates PI3Kâ Akt signal pathway by functioning as a ceRNA and predicts poor prognosis in colorectal cancer: integrative analysis of dysregulated ncRNA-associated ceRNA network

description: Additional file 4. RNAs correlated with overall survival in the ceRNA network.
DOI: 10.6084/m9.figshare.17120411
title: Additional file 3 of Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data

description: Additional file 3. Conserved and rewired targets associated with miR-17/92 family.
DOI: 10.6084/m9.figshare.17120417.v1
title: Additional file 4 of Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data

description: Additional file 4. Enrichment analysis of the rewired miRNA-mRNA modules associated with miR-17/92 family.
DOI: 10.6084/m9.figshare.17120423
title: Additional file 5 of Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data

description: Additional file 5. Cell-cell crosstalk networks.
DOI: 10.6084/m9.figshare.8207522
title: Additional file 10: of Novel secretome-to-transcriptome integrated or secreto-transcriptomic approach to reveal liquid biopsy biomarkers for predicting individualized prognosis of breast cancer patients

description: Table S2. Basal-Specific Secreted ProteinsR2. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.15020636.v1
title: Additional file 1 of Investigating causal relationships between exposome and human longevity: a Mendelian randomization analysis

description: Additional file 1: Table S1. Details of the instruments used as proxy risk factors for longevity. Table S2. Description of independent exposure GWAS used in validation. Table S3. Estimates of inverse variance weighted method for significant associations between genetically predicted exposures and longevity. Table S4. Sensitivity analysis results for the metabolites identified in secondary analysis. Table S5. Pleiotropy and heterogeneity analyses for the association between exposures and Alzheimer's disease in secondary analysis. Table S6. The Mendelian randomization association of individual SNPs of screening traits in primary analysis. Table S7. Mendelian randomization results of validation using independent exposure GWAS. Table S8. Mendelian randomization results of validation using dataset of 90th percentile longevity. Table S9. Mendelian randomization results of validation using dataset of 99th percentile longevity. Table S10. List of exposures in the present study. Table S11. Exposures identified significantly and suggestively associated with 90th percentile longevity in primary analyses. Table S12. Exposures identified significantly and suggestively associated with 99th percentile longevity in secondary analyses.
DOI: 10.6084/m9.figshare.12926249
title: Additional file 1 of IFN-α confers epigenetic regulation of HBV cccDNA minichromosome by modulating GCN5-mediated succinylation of histone H3K79 to clear HBV cccDNA

description: Additional file 1: Supplementary information. Table S1. List of antibodies used in this paper. Table S2. The characteristics of paracancerous liver tissues of HCC patients. Table S3. List of primers used in this paper. Fig S1. Succinylation of histone H3K79 contributes to the transcription of HBV DNA. (a) The efficiency of H3 overexpression was validated by Western blot analysis in HepaRG and HepG2 cells. (b) The efficiency of knockdown and overexpression of GCN5 was validated by Western blot analysis in HepaRG and HepG2 cells. (c-e) shGCN5 was transduced into HBV-infected HepaRG cells in 100-mm dishes for 5 days. GCN5 or GCN5Y645mut was transduced into HBV-infected HepaRG cells in 100-mm dishes for 6 days. The cells were harvested and used for ChIP assays with the indicated antibodies. Levels of the specific proteins on HBV cccDNA were analysed by ChIP-qPCR. The mean ± SD of at least three experiments is shown. *P &lt; 0.05, **P &lt; 0.01. Abbreviation: N.S., not significant. Fig S2. GCN5 is responsible for the succinylation of histone H3K79 on HBV cccDNA minichromosome. The efficiency of siGCN5 was validated by Western blot analysis in 293T, HepaRG and HepG2 cells. Fig S3. Relative mRNA levels of GCN5 were detected by RT-qPCR in cccDNA-positive paracancerous liver tissues (n=15) and cccDNA-negative paracancerous liver tissues (n=15). *P &lt; 0.05, **P &lt; 0.01, ***P &lt;0.001. Fig S4. IFN-α depresses the succinylation of histone H3K79 on HBV cccDNA minichromosome. (a) HepaRG cells were infected with HBV at an MOI of 600 vp/cell and treated with IFN-α for 3 days at the indicated dose. The levels of histone H3K27 acetylation and histone H3K79 succinylation were measured by Western blot analysis in the cells. (b) Histone H3K27 acetylation and histone H3K79 succinylation on cccDNA were assessed by ChIP-qPCR in the cells. (c) HepaRG cells with depleted endogenous GCN5 and reconstituted expression of wild-type flag-GCN5 or flag-GCN5Y645mut were infected with HBV at an MOI of 600 vp/cell and treated with IFN-α for 3 days at the indicated dose. Histone H3K79 succinylation on cccDNA was assessed by ChIP-qPCR in the cells. (d, e, f) The levels of HBeAg, HBsAg, and HBV DNA were analysed by ELISA and qPCR assays in the supernatant of medium from HepaRG cells. The mean ± SD of at least three experiments is shown. Statistically significant differences are indicated as follows: **P&lt;0.01; ***P&lt;0.001. Fig S5. The original raw images of Western blot analysis (a-f) and Southern blot analysis (g) in figures or supplementary figures.
DOI: 10.6084/m9.figshare.12926249.v1
title: Additional file 1 of IFN-α confers epigenetic regulation of HBV cccDNA minichromosome by modulating GCN5-mediated succinylation of histone H3K79 to clear HBV cccDNA

description: Additional file 1: Supplementary information. Table S1. List of antibodies used in this paper. Table S2. The characteristics of paracancerous liver tissues of HCC patients. Table S3. List of primers used in this paper. Fig S1. Succinylation of histone H3K79 contributes to the transcription of HBV DNA. (a) The efficiency of H3 overexpression was validated by Western blot analysis in HepaRG and HepG2 cells. (b) The efficiency of knockdown and overexpression of GCN5 was validated by Western blot analysis in HepaRG and HepG2 cells. (c-e) shGCN5 was transduced into HBV-infected HepaRG cells in 100-mm dishes for 5 days. GCN5 or GCN5Y645mut was transduced into HBV-infected HepaRG cells in 100-mm dishes for 6 days. The cells were harvested and used for ChIP assays with the indicated antibodies. Levels of the specific proteins on HBV cccDNA were analysed by ChIP-qPCR. The mean ± SD of at least three experiments is shown. *P &lt; 0.05, **P &lt; 0.01. Abbreviation: N.S., not significant. Fig S2. GCN5 is responsible for the succinylation of histone H3K79 on HBV cccDNA minichromosome. The efficiency of siGCN5 was validated by Western blot analysis in 293T, HepaRG and HepG2 cells. Fig S3. Relative mRNA levels of GCN5 were detected by RT-qPCR in cccDNA-positive paracancerous liver tissues (n=15) and cccDNA-negative paracancerous liver tissues (n=15). *P &lt; 0.05, **P &lt; 0.01, ***P &lt;0.001. Fig S4. IFN-α depresses the succinylation of histone H3K79 on HBV cccDNA minichromosome. (a) HepaRG cells were infected with HBV at an MOI of 600 vp/cell and treated with IFN-α for 3 days at the indicated dose. The levels of histone H3K27 acetylation and histone H3K79 succinylation were measured by Western blot analysis in the cells. (b) Histone H3K27 acetylation and histone H3K79 succinylation on cccDNA were assessed by ChIP-qPCR in the cells. (c) HepaRG cells with depleted endogenous GCN5 and reconstituted expression of wild-type flag-GCN5 or flag-GCN5Y645mut were infected with HBV at an MOI of 600 vp/cell and treated with IFN-α for 3 days at the indicated dose. Histone H3K79 succinylation on cccDNA was assessed by ChIP-qPCR in the cells. (d, e, f) The levels of HBeAg, HBsAg, and HBV DNA were analysed by ELISA and qPCR assays in the supernatant of medium from HepaRG cells. The mean ± SD of at least three experiments is shown. Statistically significant differences are indicated as follows: **P&lt;0.01; ***P&lt;0.001. Fig S5. The original raw images of Western blot analysis (a-f) and Southern blot analysis (g) in figures or supplementary figures.
DOI: 10.6084/m9.figshare.15020723.v1
title: Additional file 1 of Analyzing the gonadal transcriptome of the frog Hoplobatrachus rugulosus to identify genes involved in sex development

description: Additional file 1.
DOI: 10.6084/m9.figshare.7158980.v1
title: supplementary material.csv

description: We have presented the parameters of every nanostructure (long axis and short axis) we design for the chromatic metalens as well as the achromatic counterpart in the supplementary material.
DOI: 10.6084/m9.figshare.24987722
title: Additional file 1 of ANGPTL4 accelerates ovarian serous cystadenocarcinoma carcinogenesis and angiogenesis in the tumor microenvironment by activating the JAK2/STAT3 pathway and interacting with ESM1

description: Additional file 1:  Fig. S1. Prognostic significance of ARGs in OC patients. A Prognostic models were constructed by LASSO regression based on ARGs. B Lambda on abscissa, coefficients on ordinate. C The survival times, risk score, and signature expression in OC patients. D Overall survival analysis for OC patients with high or low risk. E ROC curves for survival analysis. F Correlation analysis between the risk score and immune cell infiltration. *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001. Fig. S2. Hub prognostic ARGs in OC.  Uni_cox (A) and Mult_cox (B) for 13 signatures in OC. Overall survival significance confirmed by the nomogram (C) and calibration curve (D). Drug sensitivity analysis for EGF, ANGPTL4, RUNX1, PLG, and NOTCH4 in the CTRP database (E) and GDSC database (F). PCR analysis (G) for the level of ANGPTL4 and ESM1 in SKOV3 treated with different doses of bevacizumab *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001. Fig. S3. The expression of ANGPTL4 in pan-carcinoma based TCGA database and GTEx database. The blue is for normal tissue samples and the red is for cancer samples.  Fig. S4. The expression of downstream genes in HeyA8 cells after ANGPTL4 overexpression.  A  ANGPTL4 expression confirmed in Hey-A8 cells by IF staining.  B  Volcano plot for DEG expression after ANGPTL4 overexpression by RNA sequencing. C  Heatmaps for DEG expression. D GSVA analysis and E  KEGG analysis for 14 DEGs.  Fig. S5. The level of free ANGPTL4 in CM. Free ANGPTL4 expression confirmed in the CM of SKOV3 and Hey-A8 cells by ELISA. *P &lt; 0.05.  Fig. S6. ESM1 was a key factor in the downstream of JAK-STAT pathway.  A  The expression of ESM1 in SKOV3-DMSO, SKOV3-Colivelin, Hey-A8-DMSO, and Hey-A8-AG490 groups. B  The effect of ESM1 on the angiogenesis ability of OC induced by JAK inhibitor/activator. C  The effect of ANGPTL4 on ESM1 expression. D  Co-IP showed the effects of JAK activator Colivelin on the interaction between ANGPTL4 and ESM1 in SKOV3 cells. Fig. S7. The ANGPTL4/ESM1 axis promotes OC growth and angiogenesis in vivo.  A  Morphological observation, HE and IHC staining of xenografts in the vector-SKOV3, ANGPTL4 KD-SKOV3, ANGPTL4 KD-SKOV3 with ESM1 OE, vector-HeyA8, ANGPTL4 OE-HeyA8, and ANGPTL4 OE-HeyA8 with ESM1 OE groups. B  The tumor weight and volume and the IHC staining score of xenografts in the vector-SKOV3, ANGPTL4 KD-SKOV3, ANGPTL4 KD-SKOV3 with ESM1 OE, vector-HeyA8, ANGPTL4 OE-HeyA8, and ANGPTL4 OE-HeyA8 with ESM1 OE groups. *P &lt; 0.05.
DOI: 10.6084/m9.figshare.24987722.v1
title: Additional file 1 of ANGPTL4 accelerates ovarian serous cystadenocarcinoma carcinogenesis and angiogenesis in the tumor microenvironment by activating the JAK2/STAT3 pathway and interacting with ESM1

description: Additional file 1:  Fig. S1. Prognostic significance of ARGs in OC patients. A Prognostic models were constructed by LASSO regression based on ARGs. B Lambda on abscissa, coefficients on ordinate. C The survival times, risk score, and signature expression in OC patients. D Overall survival analysis for OC patients with high or low risk. E ROC curves for survival analysis. F Correlation analysis between the risk score and immune cell infiltration. *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001. Fig. S2. Hub prognostic ARGs in OC.  Uni_cox (A) and Mult_cox (B) for 13 signatures in OC. Overall survival significance confirmed by the nomogram (C) and calibration curve (D). Drug sensitivity analysis for EGF, ANGPTL4, RUNX1, PLG, and NOTCH4 in the CTRP database (E) and GDSC database (F). PCR analysis (G) for the level of ANGPTL4 and ESM1 in SKOV3 treated with different doses of bevacizumab *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001. Fig. S3. The expression of ANGPTL4 in pan-carcinoma based TCGA database and GTEx database. The blue is for normal tissue samples and the red is for cancer samples.  Fig. S4. The expression of downstream genes in HeyA8 cells after ANGPTL4 overexpression.  A  ANGPTL4 expression confirmed in Hey-A8 cells by IF staining.  B  Volcano plot for DEG expression after ANGPTL4 overexpression by RNA sequencing. C  Heatmaps for DEG expression. D GSVA analysis and E  KEGG analysis for 14 DEGs.  Fig. S5. The level of free ANGPTL4 in CM. Free ANGPTL4 expression confirmed in the CM of SKOV3 and Hey-A8 cells by ELISA. *P &lt; 0.05.  Fig. S6. ESM1 was a key factor in the downstream of JAK-STAT pathway.  A  The expression of ESM1 in SKOV3-DMSO, SKOV3-Colivelin, Hey-A8-DMSO, and Hey-A8-AG490 groups. B  The effect of ESM1 on the angiogenesis ability of OC induced by JAK inhibitor/activator. C  The effect of ANGPTL4 on ESM1 expression. D  Co-IP showed the effects of JAK activator Colivelin on the interaction between ANGPTL4 and ESM1 in SKOV3 cells. Fig. S7. The ANGPTL4/ESM1 axis promotes OC growth and angiogenesis in vivo.  A  Morphological observation, HE and IHC staining of xenografts in the vector-SKOV3, ANGPTL4 KD-SKOV3, ANGPTL4 KD-SKOV3 with ESM1 OE, vector-HeyA8, ANGPTL4 OE-HeyA8, and ANGPTL4 OE-HeyA8 with ESM1 OE groups. B  The tumor weight and volume and the IHC staining score of xenografts in the vector-SKOV3, ANGPTL4 KD-SKOV3, ANGPTL4 KD-SKOV3 with ESM1 OE, vector-HeyA8, ANGPTL4 OE-HeyA8, and ANGPTL4 OE-HeyA8 with ESM1 OE groups. *P &lt; 0.05.
DOI: 10.6084/m9.figshare.12924131
title: Additional file 1 of Developmental stage-specific A-to-I editing pattern in the postnatal pineal gland of pigs (Sus scrofa)

description: Additional file 1 Summary of the identified A-to-I editing sites in the Sus scrofa pineal gland.
DOI: 10.6084/m9.figshare.9783401
title: Additional file 1: of LncRNA SATB2-AS1 inhibits tumor metastasis and affects the tumor immune cell microenvironment in colorectal cancer by regulating SATB2

description: Table S1. SiRNAs and sh-RNAs sequence. Table S2. The list of primers and probes. Table S3. Information of antibodies. (ZIP 44 kb)
DOI: 10.6084/m9.figshare.9783401.v1
title: Additional file 1: of LncRNA SATB2-AS1 inhibits tumor metastasis and affects the tumor immune cell microenvironment in colorectal cancer by regulating SATB2

description: Table S1. SiRNAs and sh-RNAs sequence. Table S2. The list of primers and probes. Table S3. Information of antibodies. (ZIP 44 kb)
DOI: 10.6084/m9.figshare.9783404
title: Additional file 10 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: Table S3. This table contains 8061 genes and 638624 links, and the Pearson correlation coefficients. (CSV 27,996 kb)
DOI: 10.6084/m9.figshare.9783404.v1
title: Additional file 10 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: Table S3. This table contains 8061 genes and 638624 links, and the Pearson correlation coefficients. (CSV 27,996 kb)
DOI: 10.6084/m9.figshare.9783416
title: Additional file 11 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: Table S4. This table contains gene age for 8061 different genes in original partitions. (XLSX 138 kb)
DOI: 10.6084/m9.figshare.9783416.v1
title: Additional file 11 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: Table S4. This table contains gene age for 8061 different genes in original partitions. (XLSX 138 kb)
DOI: 10.6084/m9.figshare.9783425
title: Additional file 1 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: Table S1. This table contains gene origination mechanism for 8061 different genes. In this table, ‘Dl’, ‘D’, ‘Rl’ and ‘R’ all mean genes generated by duplication mechanism. ‘A’ and ‘Al’ mean genes generated by de novo mechanisms. There is only one gene we cannot find its origination and we regard it as a de novo gene. The reference data of gene origination mechanism is downloaded from reference [30] ( http://gentree.ioz.ac.cn/index.php ). (XLSX 239 kb)
DOI: 10.6084/m9.figshare.9783425.v1
title: Additional file 1 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: Table S1. This table contains gene origination mechanism for 8061 different genes. In this table, ‘Dl’, ‘D’, ‘Rl’ and ‘R’ all mean genes generated by duplication mechanism. ‘A’ and ‘Al’ mean genes generated by de novo mechanisms. There is only one gene we cannot find its origination and we regard it as a de novo gene. The reference data of gene origination mechanism is downloaded from reference [30] ( http://gentree.ioz.ac.cn/index.php ). (XLSX 239 kb)
DOI: 10.6084/m9.figshare.9783434
title: Additional file 2 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: R code for running evolutionary model 1. This R code is for running evolutionary model 1 when the number of new genes in each step is known. (R 11 kb)