Assays

RNA-seq data for In vivo 7 samples. Only 32 RNA samples from liver of male fish sequenced. Illumina poly(A)-RNA sequencing at UiB GCF, as in Yadetie et al., 2018.

The associated zip files contains all input files and a Jupyter notebook to rerun sampled simmulations, combined simmulations, parameter scan for the model with addition of an oxygin inhibiton of LDH, local- and global-sensitivity analysis and plot simmulation output in various formats. In addition the zip file contains the py36.yaml file that can be used to recreate the model simmulation environment using Anaconda making all simmulations completely reproducable.
All information on how to use
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Simulation of OE mutants targetting enzymes in the model, combined with metabolite concentrations and enzyme fold change of from the 40 samples. For each second mutant the enzyme concentrations in case of OE and KO mutants in updated and the metabolite concentrations of the second sample are loaded in the model.
Using this approach the model approximately predicts combinatorial effects of OE mutations with other mutations, perturbations and time series concentrations.

Simple overview of all samples used for training, internal validation by copasi en external validation.
Overview of samples metadata, mean metabolite concentration and enzyme concentrations used in the model.
Only metabolites present in the model are shown.

Metabolic control analysis:
Local control coefficients for 40 independent samples based on 100x sampling from the measurement distribution
Global control analysis based on 100.000 Latin Hypercube sampling from the parameter search range (0.01-100 for Km values and 0.001-1000 for Vmax values)

Measurements of external metabolites based on growth curve data.
Flux estimates for uptake of external metabolites such as glucose and production rates for external metabolites lactate and acetate

Metabolomics time series measurements for internal metabolites for 6h, 24h and 48h for multiple experiments. Largely based on MAss spectrometry, bioluminescence kits to measure NAD, NADH at 24h, other time points are infered from relative measurements times the absolute measurements at 24h.

Protein copy number at 6h, 12h, 24h, 48h, 72h, 96h, average values and SD for the measurements

Validation by simulating independent OE, KO mutant and perturbation samples, using sampling of the gausian distribution based on the mean and SD of measurements per sample. A 1000 samples of the gausian distribution of the mean and SD was performed per sample to show error in the measurements and how it propegates in predicted metabolite concentration in SS

Training of the model, parameter estimation using Evolutionary Programming using metabolomics, proteomics and some flux data.

Empty assay

Assay: _A_01_evigene
Short Name: 01_evigene
Assay Class: DRY
Assay Type: evigene
Title: EvidentialGene tr2aacds.pl VERSION 2016.07.11
Description: See http://eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Assay: _A_02.1_BUSCO
Short Name: 02.1_BUSCO
Assay Class: DRY
Assay Type: BUSCO
Title: BUSCO on assemblies and tr2aacds output
Description: BUSCO on assemblies and tr2aacds output
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Assay: _A_02.3_InterProScan
Short Name: 02.3_InterProScan
Assay Class: DRY
Assay Type: InterProScan
Title: InterProScan on tr2aacds output
Description: InterProScan on tr2aacds output
pISA Assay creation date: 2019-10-22
pISA Assay creator: Marko Petek
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Assay: _A_02.2_assembly-contribution-count
Short Name: 02.2_assembly-contribution-count
Assay Class: DRY
Assay Type: count
Title: assembly contribution count
Description: assembly contribution count, input/output tr2aacds
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Assay: _A_02.4_STAR
Short Name: 02.4_STAR
Assay Class: DRY
Assay Type: STAR
Title: mapping reads back to evigene .tr output
Description: mapping reads back to evigene .tr output using STAR to check the percentage of reads that map
pISA Assay creation date: 2019-10-22
pISA Assay creator: Marko Petek
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Assay: _A_02.5_STARlong_matchAnnot
Short Name: 02.5_STARlong_matchAnnot
Assay Class: DRY
Assay Type: matchAnnot
Title: potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations
Description: potato initial transcriptome (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations
pISA Assay creation date: 2019-10-22
pISA Assay creator: Marko Petek
Phenodata: None
Featuredata: None
...

Assay: _A_02.6_TransRate
Short Name: 02.6_TransRate
Assay Class: DRY
Assay Type: TransRate
Title: TransRate stat on raw tr2aacds transcriptomes
Description: TransRate stat on raw (initial) tr2aacds transcriptomes, basic and reference-based
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: Nonde
Data: see ./input/path_to_files.txt

Assay: _A_02.7_VecScreen
Short Name: 02.7_VecScreen
Assay Class: DRY
Assay Type: VecScreen
Title: VecScreen on raw tr2aacds output
Description: VecScreen (contamination screening) and blastn (contaminants annotation) on raw (initial) tr2aacds output
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Assay: _A_02.8_DIAMOND
Short Name: 02.8_DIAMOND
Assay Class: DRY
Assay Type: DIAMOND
Title: DIAMOND on raw tr2aacds output
Description: DIAMOND on raw tr2aacds output, both .cds and .tr; including lost and found
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Assay: _A_04_TransRate
Short Name: 04_TransRate
Assay Class: DRY
Assay Type: TransRate
Title: TransRate post filtering and reassignment
Description: TransRate post filtering and reassignment
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Assay: _A_05_BUSCO
Short Name: 05_BUSCO
Assay Class: DRY
Assay Type: BUSCO
Title: BUSCO post filtering and reassignment
Description: BUSCO post filtering and reassignment
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Assay: _A_01_evigene_1_3cvs-gffmerged
Short Name: 01_evigene_1_3cvs-gffmerged
Assay Class: DRY
Assay Type: gffmerged
Title: tr2aacds on cv rep and gffmerged
Description: tr2aacds on cv rep and gffmerged
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Assay: _A_04-MSA
Short Name: 04-MSA
Assay Class: DRY
Assay Type: MSA
Title: Multiple sequence alignment, pantranscriptomes' paralogue clusters
Description: Multiple sequence alignment, pantranscriptomes' paralogue clusters
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Assay: _A_05_BUSCO-Stat
Short Name: 05_BUSCO-Stat
Assay Class: DRY
Assay Type: Stat
Title: BUSCO plots
Description: BUSCO plots
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Analyst: Maja Zagorscak
Phenodata: None
Featuredata:
Data:

Assay: _A_03_BUSCO_1_3cvs-gffmerged
Short Name: 03_BUSCO_1_3cvs-gffmerged
Assay Class: DRY
Assay Type: gffmerged
Title: BUSCO on pantranscriptome
Description: BUSCO on pantranscriptome
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

Assay: _A_02_components_1_3cvs-gffmerged
Short Name: 02_components_1_3cvs-gffmerged
Assay Class: DRY
Assay Type: gffmerged
Title: paralogue clusters on pantranscriptome
Description: paralogue clusters on pantranscriptome
pISA Assay creation date: 2019-10-22
pISA Assay creator: Ziva Ramsak
Phenodata: None
Featuredata:
Data:

Assay: _A_03.2_components
Short Name: 03.2_components
Assay Class: DRY
Assay Type: components
Title: Components: tr2aacds headers, cdhit-2d
Description: Components: tr2aacds headers, cdhit-2d; post-filtering redefinition of paralogue clusters
pISA Assay creation date: 2019-10-22
pISA Assay creator: Ziva Ramsak
Phenodata: None
Featuredata:
Data:

Assay: _A_03.1_filtering
Short Name: 03.1_filtering
Assay Class: DRY
Assay Type: filtering
Title: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs
Description: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt