ZF Variation

Zinc Finger Variation

Nadimpalli S, Persikov AV, Singh M (2015) Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet 11(3): e1005011. doi: 10.1371/journal.pgen.1005011

These images are reproduced from FlyBase.org and are © Nicolas Gompel.

Peptide, CDS, & Domain Files

Species	Peptide Files (aa)	CDS Files (nuc)	ZF Domains (tsv)
D. melanogaster	dmel-all-translation-r6.01.fasta.gz	dmel-all-CDS-r6.01.fasta.gz	Drosophila_melanogaster.r6.01_ZF.fulldom
D. sechellia	dsec-all-translation-r1.3.fasta.gz	dsec-all-CDS-r1.3.fasta.gz	Drosophila_sechellia.r1.3_ZF.fulldom
D. simulans	dsim-all-translation-r1.4.fasta.gz dsim-w501-pep.fa.gz	dsim-all-CDS-r1.4.fasta.gz dsim-w501-cds.fa.gz	Drosophila_simulans.r1.4_ZF.fulldom
D. yakuba	dyak-all-translation-r1.3.fasta.gz	dyak-all-CDS-r1.3.fasta.gz	Drosophila_yakuba.r1.3_ZF.fulldom
D. erecta	dere-all-translation-r1.3.fasta.gz	dere-all-CDS-r1.3.fasta.gz	Drosophila_erecta.r1.3_ZF.fulldom
D. ananassae	dana-all-translation-r1.3.fasta.gz	dana-all-CDS-r1.3.fasta.gz	Drosophila_ananassae.r1.3_ZF.fulldom
D. pseudoobscura	dpse-all-translation-r3.2.fasta.gz	dpse-all-CDS-r3.2.fasta.gz	Drosophila_pseudoobscura.r3.2_ZF.fulldom
D. persimilis	dper-all-translation-r1.3.fasta.gz	dper-all-CDS-r1.3.fasta.gz	Drosophila_persimilis.r1.3_ZF.fulldom
D. willistoni	dwil-all-translation-r1.3.fasta.gz	dwil-all-CDS-r1.3.fasta.gz	Drosophila_willistoni.r1.3_ZF.fulldom
D. grimshawi	dgri-all-translation-r1.3.fasta.gz	dgri-all-CDS-r1.3.fasta.gz	Drosophila_grimshawi.r1.3_ZF.fulldom
D. virilis	dvir-all-translation-r1.2.fasta.gz	dvir-all-CDS-r1.2.fasta.gz	Drosophila_virilis.r1.2_ZF.fulldom
D. mojavensis	dmoj-all-translation-r1.3.fasta.gz	dmoj-all-CDS-r1.3.fasta.gz	Drosophila_mojavensis.r1.3_ZF.fulldom

1-to-1 Ortholog Groups

Original FlyBase File: gene_orthologs_fb_2014_04.tsv.gz
Augmented and Reconciled: drosophila-zforthologs-1to1.tsv

Pairwise Alignments by Orthogroup

Peptide Alignments: drosophila-pepalns.tar.gz
Codon Alignments: drosophila-codonalns.tar.gz

Sets of Conserved & Diverged ZF Genes

Set 1. Conserved across all 12 species
	cons1.txt (47 genes)
	sm-bp	sm-mf	sm-cc
	nsm-bp	nsm-mf	nsm-cc
*Set 2. Conserved across all species in which a 1-to-1 ortholog is present
	cons2.txt (82 genes)
	sm-bp	sm-mf	sm-cc
	nsm-bp	nsm-mf	nsm-cc
Set 3. Found in all 12 species; diverged in 1+ domains
	div1.txt (101 genes)
	sm-bp	sm-mf	sm-cc
	nsm-bp	nsm-mf	nsm-cc
Set 4. Diverged in 1+ domains
	div2.txt (196 genes)
	sm-bp	sm-mf	sm-cc
	nsm-bp	nsm-mf	nsm-cc
Set 5. Diverged in 2+ domains
	div3.txt (182 genes)
	sm-bp	sm-mf	sm-cc
	nsm-bp	nsm-mf	nsm-cc
*Set 6. Diverged in 1+ domains in 2+ species
	div4.txt (181 genes)
	sm-bp	sm-mf	sm-cc
	nsm-bp	nsm-mf	nsm-cc
Set 7. Diverged in 2+ domains in 2+ species
	div5.txt (130 genes)
	sm-bp	sm-mf	sm-cc
	nsm-bp	nsm-mf	nsm-cc
Set 8. Diverged in 1+ canonically-linked domains
	div6.txt (155 genes)
	sm-bp	sm-mf	sm-cc
	nsm-bp	nsm-mf	nsm-cc

*Used in GO Term Enrichment Analysis in S4 Table.
sm = GO term annotations inferred from sequence models included
nsm = GO term annotations inferred from sequence models not included
bp = biological process
mf = molecular function
cc = cellular component

Supplemental Tables

S1 Table. Divergent residue counts and significance values.
S2 Table. Percent of correctly-predicted columns by consensus predictions.
S3 Table. Binding specificity change from reference (as measured by PCC) for various confidence thresholds.
S4 Table. Enrichment of Gene Ontology terms by GO TermFinder.
S5 Table. C2H2-ZF domains by species.
S6 Table. Augmented and reconciled orthogroups.

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