Neurospora crassa metabolic model
Sara Calhoun
Generated August 19, 2020

Neurospora crassa metabolic modeling and genome analysis

Here, we've imported datasets to enable analyses in KBase narratives. We've imported the published metabolic model of Neurospora crassa, which was built, manually curated, and validated by Dreyfuss et al. The genome of Neurospora crassa was retrieved from NCBI RefSeq (GCF_000182925.2) and was sequenced by the Broad Institute. Gene expression data was produced by the Joint Genome Institute and described in the publication by Wu et al.

Furthermore, genome analysis tools and datasets can be accessed at the MycoCosm portal page: https://mycocosm.jgi.doe.gov/Neucr2/Neucr2.home.html

References:

  • Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE. Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PLoS Comput Biol. 2013;9(7):e1003126. doi:10.1371/journal.pcbi.1003126
  • Galagan JE, et al. The genome sequence of the filamentous fungus Neurospora crassa. Nature. 2003;422(6934):859-68. doi: 10.1038/nature01554.
  • Wu VW, et al. The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus. PNAS. 2020;117(11):6003-6013. doi:10.1073/pnas.1915611117

Metabolic model of N. crassa

iJDZ836_KBase
v13 - KBaseFBA.FBAModel-11.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/65178

Flux balance analysis run on the N. crassa metabolic model

Run Flux Balance Analysis
Use flux balance analysis to predict metabolic fluxes in a metabolic model of an organism grown on a given media.
This app completed without errors in 1m 33s.
Objects
Created Object Name Type Description
iJDZ836_FBA FBA FBA-13 iJDZ836_FBA
Report
Summary
A flux balance analysis (FBA) was performed on the metabolic model 65178/5/13 growing in 65178/6/1 media.
Output from Run Flux Balance Analysis
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/65178

N. crassa genome imported into KBase

iJDZ836.genome
v1 - KBaseGenomes.Genome-8.2
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/65178

Species tree

Insert Genome Into SpeciesTree - v2.2.0
Add one or more Genomes to a KBase SpeciesTree.
This app completed without errors in 3m 41s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/65178
  • Species_tree_ncrassa.newick
  • Species_tree_ncrassa-labels.newick
  • Species_tree_ncrassa.png
  • Species_tree_ncrassa.pdf

Gene expression profiling in conditions ranging from simple sugars to complex carbohydrates

Import TSV File as Expression Matrix From Staging Area
Import a TSV file from your staging area into your Narrative as an Expression Matrix
This app completed without errors in 49s.
Summary
Import Finished Expression Matrix Object Name: ncrassa_transcriptome_kbase.tsv_matrix Imported TSV File: ncrassa_transcriptome_kbase.tsv
ncrassa_transcriptome_kbase.tsv_matrix
v1 - KBaseFeatureValues.ExpressionMatrix-1.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/65178

Apps

  1. Import TSV File as Expression Matrix From Staging Area
    no citations
  2. Insert Genome Into SpeciesTree - v2.2.0
    • Price MN, Dehal PS, Arkin AP. FastTree 2 Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One. 2010;5. doi:10.1371/journal.pone.0009490
  3. Run Flux Balance Analysis
    • Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010;28: 977 982. doi:10.1038/nbt.1672
    • Orth JD, Thiele I, Palsson B . What is flux balance analysis? Nature Biotechnology. 2010;28: 245 248. doi:10.1038/nbt.1614