Code and data for Homologous nodes in annotated complex networks

About:

This is a repository for all code, analysis and data accompanying the Moon & Ahnert paper.

Installation:

• Run:

conda env create -f vectorisation.yml
conda activate vectorisation_env

• Download the data folder from [here] and add to this directory.
• Then run Jupyter notebooks to do analysis and generate figures into the figures folder.

Note:

• Requires Graphviz to be installed for dot layout in networkx (see here) - the yml file should handle this.

Contents:

data

Please download from the Zenodo link above and save into the repository directory.

/grn: Graph regulatory network and associated metadata

• /gene_association.tair is the gene ontology (GO) annotations associated with each gene downloaded from The Arabidopsis Information Resource (TAIR), Berardini et al., Plant Physiology (2004). Version generated: 2025-01-01.
• /AtRegNet.csv is the gene regulatory network of the Arabidopsis Thalania, available from agris, Palaniswamy et al., Plant Physiology (2006). Version dated: 2019-03-11.
• /tf_family.csv Transcription factor gene list for family annotation metadata from AtTFDB in agris, Palaniswamy et al., Plant Physiology (2006).
• /ATH_GO_GOSLIM.txt is the gene ontology annotation explanatory text file, downloaded from The Arabidopsis Information Resource (TAIR), Berardini et al., Plant Physiology (2004). Version generated: 2025-03-01.

/foodweb : ecological food web network and associated metadata

• /florida.bare_upto122_fullnames is a text file of the prey to predator edge list, from Heymans et al., Ecological Modelling, (2002).
• florida.bare_upto122_fullnames.newcat.terms is a text file of the organism and organism type annotations, from Heymans et al., Ecological Modelling, (2002).

/recipe : cuisine, ingredient and recipe mulitpartite network

• /cuisine_recipe is a text file of cuisines types and the recipe IDs that belong to the cuisine, from allrecipes recipe database, via Ahn et al., Scientific Reports, (2011).
• /recipe_ingredients_bipartite is a text file containing the edge list of recipe IDs to cuisine labels, from allrecipes recipe database, via Ahn et al., Scientific Reports, (2011).
• /foodtype_categorised.csv is a csv of manual categorisation of ingredient type.
• /cuisine_geo_labels.csv is a csv of manual cuisine categorisation into geographical regions of origin.

Enriched clusters in the GRN

• The full .csv file of the enriched clusters, their TF family labels, and the GO slim descriptors can be found in grn_GO_enrichment.csv, (also in data/grn/grn_GO_enrichment.csv).

src

• ipynb notebooks are here. Recommended to run in order of numbering.
  • 00_visualisation.ipynb visualises the multipartite recipe network. Figure 3C.
  • 01_vectorisation.ipynb performs the connectivity aggregation and vectorisation for the three networks. Saves these vectors (optional) into a processed subfolder in data/*/.
  • 02_clustering.ipynb clusters and visualises these clusters into a dendrogram and associated vector heatmap. Figures 2(A,B), 3(A,B), 4(A), 5, S1, S2, S3.
    • For the gene regulatory network, it performs the enrichment analysis for the clusters of transcription factors.
  • 03_null_models_nb.ipynb includes null models of the specialization-diversity entropic vector euclidean pairwise distances for cell types, serial homologues and left-right pairs. Figures 2D, 3D, 4B, S4.
  • XX_toy_model.ipynb Includes the visualisation of the vectorisation method on a toy model network. Figure 1.

/module/

• Scripts and functions to run the analysis:
  • fvec.py: a fast vectorisation routine.
  • graphpeeler.py: helpers for probabilistic topological layer sorting.
  • enrichement_utils.py: helpers for performing GO term enrichment analysis.
  • data_prep.py: preparation of data from raw sources.
  • null_helpers.py: null model wrappers used in src/03_null_models.ipynb.

figures

• (Sub)figures are organised into their respective network folders.
• Fully annotated clustering figures are found in:
  • /fw/f3a_dendrogram_full.pdf for the food web network.
  • /rn/f4a_dendrogram_full.pdf for the recipe network.
  • /grn/s1_TF_GRN_GO_clustering_BH_all_GO_annotated.pdf for the gene regulatory network.

References

Ahn, Y.-Y., Ahnert, S. E., Bagrow, J. P., Barab´asi, A.-L., (2011) Flavor network and the principles of food pairing, Scientific Reports 1, 196

Berardini, T.Z., Mundodi, S., Reiser, R., Huala, E., Garcia-Hernandez, M., Zhang, P., Mueller, L.M., Yoon, J., Doyle, A., Lander, G., Moseyko, N., Yoo, D., Xu, I., Zoeckler, B., Montoya, M., Miller, N., Weems, D., Rhee, S.Y. (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiology 135(2):745–755.

Heymans, J.J., Ulanowicz, R.E., Bondavalli, C., (2003) Network analysis of the South Florida Everglades graminoid marshes and comparison with nearby cypress ecosystems, Ecological Modelling 149(1–2):5-23.

Palaniswamy, S.K., James, S., Sun, H., Lamb, R.S., Davuluri, R.V., Grotewold, E. (2006) AGRIS and AtRegNet: A platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiology, 140(3):818-829.