Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution

Additional file 1:

List of 314 incorrect entries (non-TFs) in C. elegans.

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Additional file 2:

List of 167 genes that encode chromatin remodeling, general transcription and DNA/RNA binding factors in C. elegans.

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Additional file 3:

List of 83 histone-encoding genes in C. elegans.

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Additional file 4:

List of 988 TF genes in C. elegans.

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Additional file 5:

List of 17 false positives in wTF2.0.

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Additional file 6:

List of 995 TF genes in C. briggsae.

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Additional file 7:

List of 1093 TF genes in C. remanei.

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Additional file 8:

List of 150 TF orthologs in Drosophila melanogaster, M. musculus, and H. sapiens.

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Additional file 9:

BLASTP hits of C. briggsae-divergent TFs in C. elegans genome.

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Additional file 10:

Tandem arrays of TF genes in C. elegans.

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Additional file 11:

Tandem arrays of TF genes in C. briggsae.

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Additional file 12:

Phylogenetic tree of NHR genes in Caenorhabditid nematode species. Colors mark NHR genes in different species (blue: C. elegans, red: C. briggsae and light green: C. remanei). Tandemly along chromosomes and phylogenetically clustered genes are indicated by vertical bars. Chromosomes carrying NHR clusters are indicated by roman numerals. The sub-branch comprised of seven groups of NHR genes on chromosome V has been marked by a star (*). Scale bar represents 0.5 substitutions per site.

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Additional file 13:

C. elegans genes and their mutant phenotypes in RNAi assays.

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Additional file 14:

RNAi phenotypes sorted into six broad categories.

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Additional file 15:

List of the worm (C. elegans) fly (D. melanogaster) and mouse (M. musculus) mutant phenotypes associated with conserved TF genes.

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Additional file 16:

List of TF genes and their interactors. The columns A and B merely list gene pairs that interact with each other and do not indicate the direction of regulation.

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