REGENOMICS

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Transcriptome analysis

Correlation heatmap Dimensionality reduction Differential expression analysis

Selected transcriptomes and/or uploaded expression data are used for correlation analysis.
Results are shown in Spearman correlation coefficients.

Click here to download a table of datasets and conditions deposited for transcriptome analysis.

Select transcriptomes for analysis

Wound-induced tissue repair
Root explant (Hernandez-Coronado et al., 2022)
Hypocotyl explant (Ikeuchi et al., 2017)
Root tip (Matosevich et al., 2020)
Leaf explant (Pan et al., 2019)
Root explant (Rymen et al., 2019)
Leaf explant (Ye et al., 2020)
Leaf explant (Zhang et al., 2019)
Hormone-induced plant regeneration
Hypocotyl callus (Coleman et al., 2020)
Root callus (Ishihara et al., 2019)
Root callus (Kim et al., 2018)
Hypocotyl callus (Lambolez et al., 2022)
Root callus (Liu et al., 2016)
Root callus (Liu et al., 2020)
Hypocotyl callus (wox5-1wox7-1) (Zhai et al., 2021)
Hypocotyl callus (plt1plt2) (Zhai et al., 2021)
Somatic embryogenesis
Immature embryo (Wang et al., 2020)
Seedling on E5 media (Wang et al., 2020)
LEC2-inducible seedling (Wang et al., 2020)
Immature embryo (Wickramasuriya et al., 2015)
Protoplast regeneration
Mesophyll protoplast (Sakamoto et al., 2021)
Mesophyll protoplast (Xu et al., 2021)
Root tip cell types and developmental zones
Root (Li et al., 2016)

Upload your expression data

- The uploaded file must contain non-normalized raw counts for
each gene (AGI locus code).

- It must be in comma-separated values (.csv) format as shown below.

- The data may contain a different number of genes than the example,
as long as genes are in the same format (e.g. AT1G01010).

Click here to download an example table of transcriptomes.
(Downloaded and processed from GSE52966)
No file selected

Selected transcriptomes and/or uploaded expression data are used for dimensionality reduction.
Dimensionality reduction is performed with principal component analysis (PCA) and multidimensional scaling (MDS).

Click here to download a table of datasets and conditions deposited for transcriptome analysis.

Select transcriptomes for analysis

Wound-induced tissue repair
Root explant (Hernandez-Coronado et al., 2022)
Hypocotyl explant (Ikeuchi et al., 2017)
Root tip (Matosevich et al., 2020)
Leaf explant (Pan et al., 2019)
Root explant (Rymen et al., 2019)
Leaf explant (Ye et al., 2020)
Leaf explant (Zhang et al., 2019)
Hormone-induced plant regeneration
Hypocotyl callus (Coleman et al., 2020)
Root callus (Ishihara et al., 2019)
Root callus (Kim et al., 2018)
Hypocotyl callus (Lambolez et al., 2022)
Root callus (Liu et al., 2016)
Root callus (Liu et al., 2020)
Hypocotyl callus (wox5-1wox7-1) (Zhai et al., 2021)
Hypocotyl callus (plt1plt2) (Zhai et al., 2021)
Somatic embryogenesis
Immature embryo (Wang et al., 2020)
Seedling on E5 media (Wang et al., 2020)
LEC2-inducible seedling (Wang et al., 2020)
Immature embryo (Wickramasuriya et al., 2015)
Protoplast regeneration
Mesophyll protoplast (Sakamoto et al., 2021)
Mesophyll protoplast (Xu et al., 2021)
Root tip cell types and developmental zones
Root (Li et al., 2016)

Upload your expression data

- The uploaded file must contain non-normalized raw counts for
each gene (AGI locus code).

- It must be in comma-separated values (.csv) format as shown below.

- The data may contain a different number of genes than the example,
as long as genes are in the same format (e.g. AT1G01010).

Click here to download an example table of transcriptomes.
(Downloaded and processed from GSE52966)
No file selected

Select two different conditions for differential expression analysis.

Conditions must be selected from the same study for analysis.

Click here to download a table of datasets used in REGENOMICS.
Click here to download a glossary of terms used in REGENOMICS.