Fuzzy query is enabled. In the main page, perturbation datasets can be quickly searched by gene symbol, gene ID, perturbation Type (knockdown, knockout or overexpression), phenotype or data type (RNA-Seq, scRNA-Seq or microarray).

Perturbation datasets meeting the criteria are listed. Clicking on the dataset ID will lead to the detailed information page.

If more than 1 perturbation dataset were found, further overlapping analysis will be provided. The overlapping downstream DEGs of gene perturbations will be shown in a network, while common functions/pathways of perturbed genes will be analyzed.

The detailed information page contains the available perturbation information, altered phenotypes, differential genes, enriched regulations/functions/pathways, differential cell type markers by the genetic perturbation.

Besides the overall analysis, the single-cell cluster analysis will generate the cell clustering plot with cell type annotation when available, cluster marker genes and differential genes in clusters.

The list of perturbation datasets could be viewed in an interactive table on this page. Users can customize filters using "Perturbation Type", "Data Type", "Tissue Type" and "Organism". Then users can click on "Dataset ID" to view the corresponding detailed information page.

Differential Gene Overlapping Analysis helps to investigate the perturbation datasets which are significantly enriched in the user-given gene set by hypergeometric test. It can also allow users to search DEGs in PertOrg.

Step 1: Select an organism.

Step 2: Select a gene type e.g. up-regulated gene, down-regulated gene or differential gene.

Step 3: Input the gene name(s)/ID(s), multiple items should be separated using commas, e.g., "14,18,52"

Step 4: Submit

As the results, the PertOrg datasets in which DEG list includes submitted genes are given. Hypergeometric p-values are provided for each dataset.

Dataset Enrichment Analysis helps to identify the perturbation datasets in which the user-given gene set are over-represented.

Step 1: Select an organism.

Step 2: Select a gene type e.g. up-regulated gene, down-regulated gene or differential gene.

Step 3: Input the gene name(s)/ID(s), multiple items should be separated using commas, e.g., "14,18,52"

Step 4: Submit

As the results, the PertOrg datasets in which user submitted genes are over-represented given. Enrichment scores are provided for each dataset.

In the "Statistics" page, the statistics of the perturbation datasets in multiple perspectives are illustrated.

In the Download page, the information of perturbation datasets, available DEGs, differential gene expression analysis result and gene expression profile of each dataset can be downloaded.

Although an increasing number of perturbation datasets are expected to be collected, many available datasets could still be missed. Therefore, users are encouraged to submit their dataset that meets PertOrg criteria for future integration. PertOrg allows users to submit perturbed genes, perturbation types, tissue types, data types and organisms, as well as a link to their data sources on the "Submit" page. Once the submission is received, data will be carefully evaluated and further processed using our standard procedures in PertOrg, as described in the Material and Methods section. Finally, the dataset and the corresponding analysis results will be included in the future release of PertOrg.

On the help page, the introduction of the features and the guidelines for the functions are stated. The contact details are attached at the bottom.