IPOP is a multi-omics, multi-plant database, in which dataset contains Histone Modification, Chromatin Accessibility, Chromatin Interaction, Population Genomics, DNA 5mC Modification, Transcriptome, RNA m6A Modification data, and the results of Evolutionary Genomics studies; involves 13 species. IPOP provides multiple omics results data search and download functions, and six tools for users to analyze multiple omics data.

The Browser bar on homepage Provides the ability to view genomic annotations, as well as different omics data for each species.

Figure 1 Browser module

Select the species on the browser page to enter the Jbrowse to view all the omics sequence information of the species.

The Search bar on the home page provides the ability to search by gene IDs, key words and sample IDs.

Figure 2 Search module

The figure above shows the result page of the search function, and the number of terms related to the search content is displayed at items.

The Evolutionary Genomics bar provides evolutionary information of all genes in IPOP.

Figure 3 Evolutionary genomics module

Figure 4 Phylostratigraphic Stage page

Click nodes in the phylostratigraphic tree on the index page jump to Phylostratigraphic Stage page. Phylostratigraphic Stage page provides detailed information and statistics of the phylostratigraphic stage.

Figure 5 Orthologous Groups page

Click bars of the Orthologous Groups Evolutionary Origin part and Species Orthologous Groups / Genes Information part in Evolutionary Genomics page to jump to Orthologous Group page. Orthologous Group page provides statistics of genes related to the orthogroup.

Figure 6 Duplication Event page

Click bars of Duplication Events part in Evolutionary Genomics page to jump to Duplication Event page. Duplication Event page provides detailed duplication events and mechanisms of which.

Figure 7 Gene page

Search by Orthologous groups and Evolution Origin jump to Gene page. Gene page provides detailed evolutionary information of related genes. Search by Duplication Events jump to Duplication Events page, which was introduced in 3.4.

Figure 8 Sample statistics of histone modification

The Sample statistics page shows the sample statistics of different strains and tissues, and lists the basic information of each sample.

Figure 9 Search module of histone modification

Search module of histone modification provides the ability to search for histone modification peaks using gene IDs and genome location.

Figure 10 Sample infomation page of histone modification

Sample infomation displays the basic information of the sample and the statistics of the distribution of peaks identified in the sample. The details of each peak are listed in the Histone Modification Peaks table, which is as follows:

Figure 11 Sample statistics of chromatin accessibility

The Sample statistics page shows the sample statistics of different strains and tissues, and lists the basic information of each sample.

Figure 12 Search module of chromatin accessibility

Search module of chromatin accessibility provides the ability to search for chromatin accessibility regions using gene IDs and genome location.

Figure 13 Sample infomation page of chromatin accessibility

Sample infomation displays the basic information of the sample and the statistics of the distribution of peaks identified in the sample. The details of each peak are listed in the Accessible Chromatin Regions table, which is as follows:

Figure 14 Data quality

Intersize, correlation and reads distribution of each replicate are visualized in the Data Quality part.

Figure 15 Sample statistics of chromatin interaction

The Sample statistics page shows the sample statistics of different strains and tissues, and lists the basic information of each sample.

Figure 16 Search module of chromatin interaction

Search module of chromatin interaction provides the ability to search for loop regions and tad regions using gene IDs and genome location.

Figure 17 Sample infomation page of chromatin accessibility

Sample infomation displays the basic information of the sample. The details of each loop region and tad region are listed in the tables, which are as follows:

Figure 18 Genome wide variant-trait associations’ information

The population genomics page shows the sample statistics of variant-trait associatoins and variant related traits, and lists detailed information of each significant association in Associations table, which are as follows:

Figure 19 Search module of population genomics

Search module of population genomics provides the ability to search for variant-trait associations using gene IDs and genome location.

Figure 20 Sample statistics of DNA 5mC Modification

The Sample statistics page shows the sample statistics of different strains and tissues, and lists the basic information of each sample.

Figure 21 Search module of DNA 5mC modification

Search module of DNA 5mC modification provides the ability to search for DNA 5mC modified genes using gene IDs and genome location.

Figure 22 Sample infomation page of DNA 5mC modification

Sample infomation displays the basic information of the sample. Statisitcs of each type methylation level is displayed in barplot. The details of each DNA 5mC modified gene are listed in the tables, which are as follows:

Figure 23 Data quality of DNA 5mC modification

Coverage distribution of each methylation type and genome-wide methylation level are visualized in the data quality part.

Figure 24 Sample statistics of transcriptome

The Sample statistics page shows the sample statistics of different strains and tissues, and lists the basic information of each sample.

Figure 25 Search module of transcriptome

Search module of transcriptome provides the ability to search for expression level of genes using gene IDs and genome location.

Figure 26 Sample infomation page of transcriptome

Sample infomation displays the basic information of the sample. The details of each gene are listed in the tables, which are as follows:

Figure 27 Sample statistics of RNA m6A modification

The Sample statistics page shows the sample statistics of different strains and tissues, and lists the basic information of each sample.

Figure 28 Search module of transcriptome

Search module of transcriptome provides the ability to search for m6A peaks using gene IDs and genome location.

Figure 29 Sample infomation page of RNA m6A modification

Sample infomation displays the basic information of the sample and the statistics of the distribution of peaks identified in the sample. The details of each peak are listed in the tables, which are as follows:

Figure 30 Enriched motif

Enriched motifs of m6A peaks in the sample are listed in Enriched Motif part.

Figure 31 m6A regulator candidates

Transcriptional profile of m6A regulator candidate genes is displayed in bar plot in the m6A Regulator Candidates part.

Figure 32 Data quality

Reads distribution and correlation between replicates of the sample are visualized in Data Quality part.

Figure 33 Submission of Omics Comparison Analysis Tool

The above figure shows the way of task submission and result viewing of the comparison tool. On the Submission page, click the jobID to jump to the result page. If the task is not completed, it will wait on the running page, and it will automatically jump after it is completed.

Figure 34 Sample information

Detail informaion of two compared samples is listed here.

Figure 35 Overlap of accessible chromatin regions

Overlap of Accessible Chromatin Regions plot. The green bar indicates overlapping genes of two samples, the blue bar and the yellow bar indicates unique genes of two sample respectively.

Figure 36 Distribution of accessible chromatin regions

The results page displays the accessible chromatin regions with different distances from the TSS in the form of a bar plot and the accessible chromatin regions feature distribution.

Figure 37 Sample information

Detail informaion of two compared samples is listed here.

Figure 38 Overlap of histone modification peaks

Overlap of Accessible Chromatin Regions plot. The green bar indicates overlapping genes of two samples, the blue bar and the yellow bar indicates unique genes of two sample respectively.

Figure 39 Distribution of histone modification peaks

The results page displays the histone modification peaks with different distances from the TSS and the histone modification peaks feature distribution in the form of bar plots.

Figure 40 Transcription profiles of compared m6A-seq samples

As is shown in figure 11, the transcription part of RNA m6A modification results page draws a volcano plot showing genes with significantly different expression levels. The expression of m6a-regulated candidate genes in the two samples is displayed in the form of a bar plot.

Figure 41 RNA m6A modification profiles of compared m6A-seq samples

In the modification part, the gene and peak differences of the two samples were analyzed separately, and the difference and overlapping modified genes and peaks were displayed in the form of bar plots; and the volcano plot was drawn to show the genes with significant m6a modification differences and the peaks with significant differences.

Figure 42 Differentially methylated region

The DNA methylation results page displays the differentially methylated regions in tabular form. The table details are as follows:

Figure 43 Transcription profiles of compared RNA-seq samples

The Transcriptome Results page displays different and overlapping genes between the two samples in a bar plot, and a volcano plot showing genes with significantly different expression.

Figure 44 Submission of Integrated Omics Analysis Tool

The figure above shows how to submit tasks for integration tools, which can integrate up to three omics.

Figure 45 Result of Multi-omics Integration Analysis tool

The integration tool results page lists the intersection of two omics significant regions in tabular form and visualized with a circos plot. The table details are as follows:

Figure 46 Submission of Evolutionary Information Analysis Tool

The figure above shows how the evolutionary analysis tool is used. You can enter text or upload a file to submit genes to search.

The Evolutionary Information Annotation Tool result page presents evolutionary information for the searched genes in various formats.

Figure 47 Genes evolutionary annotation

The orthologous groups and phylostratigraphic stages associated with each gene are displayed in tabular form. The table details are as follows:

Figure 48 Genes Phylostratigraphic tree

The phylostratigraphic stages involved in the genes entered by the user are marked in red in the phylostratigraphic tree.

Figure 49 Genes evolutionary origin

The number of genes at different phylostratigraphic stages is displayed in the form of a bar plot.

Figure 50 Gene related orthologous groups

The number of genes associated with different orthologous groups is displayed as a bar plot.

Figure 51 Duplication events

The bar plot shows the number of genes with different duplication event mechanisms, and the table shows the repeat mechanism of each duplicate gene pair.

Figure 52 Submission of Transcriptome-wide Association Analysis Tool

The above figure shows the usage of the twas analysis tool. Users can view the existing TWAS results in the database or analyze their own data. The content and usage of the Submission page is the same as the omics comparison analysis tool.

Figure 53 Result of Transcriptome-wide Association Analysis Tool

The TWAS results are visualized in the form of a Manhattan map, and details of the TWAS results are given in the table, and the contents of the table are as follows：

Figure 54 Submission of Phylogenetic Tree Construction tool

The Phylogenetic Tree Construction tool can be used to build an evolutionary tree using either a Fasta file or gene IDs that matches the genome version in the database.

Figure 55 Result of Phylogenetic Tree Construction tool

Figure 56 Submission of Basic Local Alignment Search tool

Figure 57 Result of Basic Local Alignment Search tool

BLAST results are displayed in the form of a table, and the contents of the table are as follows：

The Download bar on the home page provides downloads of all the result data in the database.

Figure 58 Download module