Transcription factors
From Purdue Genomics Database Facility
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Articles
- Brief History of the Selaginella genome project and taxonomy
- Contamination
analysis - Distribution of genes
- Flagellar Proteins
- Protein kinases
- transcription factors
- Evolution of developmental genes
- Meristems
- Root
- Vascular system
- Cytoskeletons
- Epidermal cell differentiation
- Pollen
- ABA
- Seed
- Ethylene
- Brassinosteroids
- Gibberellins
- Cytokinin
- Evolution of cytokinin signaling
- Auxin
- Phosphoinositides
- Evolution of auxin signaling
- Epigenetic gene regulation
- Phase transition
- Cell cycle
- Circadian clock
- Light signalling
- small RNAs
- PEBP gene family
- Potassium channels
- PPR gene family
- Cyclic Nucleotide Gated Channels
- YABBY gene family
- Ras superfamily GTPases
- LUMINIDEPENDENS (LD)
- UNUSUAL FLORAL ORGANS (UFO)
- STERILE APETALA (SAP)
- PESCADILLO - Wnt-like signaling?
- KEGG differences
- The NTMC2 genes of embryophytes
- BRK1 and apical growth
- MADS-box genes
- Lignin monomer biosynthesis
- BAHD family acyltransferases
- SCPL (serine carboxypeptidase-like) enzymes
- Cytochrome P450
- Light Harvesting Complexes
- Transcription factors involved in senescence
- Phylogenetic_Patterns
- Metallothionein
- Duplicate Gene Analyses
- HAP3 gene family
- Sucrose transporter gene family
- Hexose/hexitol transporter gene family
- Amino acid transporter gene family
- Ammonium transporter gene family
- plastidic maltose transporter gene family
- Telomeres, subtelomeres and telomere-related genes
- Sulfate transporter gene family
- proton/urea cotransporter
- Cell wall composition and glycosyltransferases involved in cell wall formation
- KNOX Genes
- Cellulose synthase superfamily
- Ubiquitin-mediated proteolysis
- Whole Genome Syntenic Analysis of Haplotypes
- Lack of Synteny Between Selaginella and Physcomitrella patens, Oryza sativa japonica, and Vitis vinifera
Transcription Associated Proteins
Based on three 2007 papers about plant transcription associated proteins (TAP, references below) we have generated a set of classification rules for plant transcription factors (TF), transcriptional regulators (TR) and putative TAPs (PT).
Riano-Pachon DM, Ruzicic S, Dreyer I, Mueller-Roeber B. PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics. 2007 Feb 7;8:42. Richardt S, Lang D, Reski R, Frank W, Rensing SA. PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. Plant Physiol. 2007 Apr;143(4):1452-66. Epub 2007 Mar 2. Guo AY, Chen X, Gao G, Zhang H, Zhu QH, Liu XC, Zhong YF, Gu X, He K, Luo J. PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Res. 2007 Oct 12; Epub ahead of print
TF Scan results
We applied the above mentioned classification rules to the Selaginella complete set of gene-model derived proteins (FM2) as well as to the non-redundant allelic variant set (FM3).
Within FM2, we found 1926 TAPs out of 34697 proteins.
Within FM3, we found 1098 TAPs out of 22285 proteins.
(i.e., on average, 57% of the TAPs are found within 64% of the proteins, if one compares FM2 to FM3)
In conclusion, there are 1098 TAPs non-redundantly representing the two haplotypes.
Family classifications (90 families) are available as well as gene model lists.
These automated annotation could be transferred to the gene models.
We can generate phylogenies for those families displaying biased size (see below), including the homologs from the genomes mentioned.
Biased family size
We compared gene family sizes with Arabidopsis, rice, poplar, grapevine, moss, C. reinhardtii, O. tauri, O. lucimarinus, T. pseudonana, P. tricornutum and C. merolae and calculated p-values for each deviating family (pair).
Gene families that significantly differ in size between Physcomitrella and Selaginella:
AP2/EREBP bHLH C2C2-Dof GRAS PHD SET
Gene families that significantly differ in size between Physcomitrella and vascular plants (vascular plant expansion):
AP2/EREBP AUX/IAA G2-like GeBP GNAT HRT MADS MYB NAC PHD Sir2 TCP Trihelix
Gene families that significantly differ in size between Selaginella/Physcomitrella and seed plants (seed plant expansion):
ABI3/VP1 AP2/EREBP AUX/IAA C2C2-Dof C2C2-YABBY DUF296 and HMG DNA-binding domain containing GeBP GNAT GRAS HB HRT HSF MADS MYB NAC Nin-like PHD PLATZ SET Sir2 SNF2 TCP Trihelix WRKY
Comparison with the data generated by Potsdam
The Mueller-Roeber group has analyzed the Selaginella TFs/TRs according to the Riano-Pachon et al. paper mentioned at the top of this page. The comparison of the Freiburg and Potsdam data, both gene- and family-wise, has been summarized in an Excel spreadsheet.
More Information
For further information and questions please contact:
stefan.rensing@biologie.uni-freiburg.de
andreas.zimmer@biologie.uni-freiburg.de
