EcoToxXplorer

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EcoToxXplorer accepts RNA-seq count data table as input. There is a standard format which needs to be followed - hover your mouse to the question mark next to Data File for more details.

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Gene-level summarization

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Differential expression examples

EE2 RNA sequencing

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Gene expression of liver tissue from Japanese quail (Coturnix japonica) under 3.3 and 33.3 (µg/g) of Ethinylestradiol exposure

Ethinylestradiol (EE2) is a model endocrine disrupting chemical. This dataset was included to give an example of RNA sequencing data analysis.

WWTP field study

Dataset Card

18 Agilent-019597 FHM_Denslow_8x15K data, normalized, log 2 scale (NCBI accession: GSE96678).

Gene expression of fathead minnow liver exposed to Ely WWTP effluent. Treatment = upstream of WWTP, WWTP effluent point source, downstream of WWTP.

Dose-response examples

Bromobenzene

Dataset Card

This dataset demonstrates dose-response analysis with microarray data from rats. (DOI 10.1007/s00204-016-1886-5)

Chemical: Bromobenzene (CAS number: 108-86-1). Doses: 25, 100, 200, 300, and 400 mkd. Tissue: Liver. Organism Rattus norvegicus (F344 rats). Sex: Male. Duration: 2 weeks.

TCDD

Dataset Card

This dataset demonstrates dose-response analysis with RNA sequencing data from mice. (DOI 10.1186/s12864-015-1527-z)

Chemical: TCDD (CAS number: ). Doses: 0.01, 0.03, 0.1, 0.3, 1, 3, 10, and 30 ug/kg. Tissue: Liver. Organism Mus musculus. Sex: Female. Duration: 4 weeks.

DE analysis can be performed on unannotated RNA-seq data in cases where annotation is not supported or to perform transcript-level DE analysis. Annotation will be required for functional analysis. Please press to confirm if you wish to analyze your data unannotated.