PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
|
Home TFext BLAST Prediction Download Help About Links PlantRegMap |
- The flowchart for construction of PlantTFDB
- Data source
- Data source (TFext)
- Pipeline to construct comprehensive protein dataset
- Family assignment rules
- List of studies which use the Family assignment rules
- Thresholds for domain identification
- Summary of TFs in different taxonomic lineages of green plants and the origination stage of TF families
- Pipeline for parsing BLAST reciprocal best hits (RBHs) and inferring orthologous groups
- Pipeline for GO annotation
- Curation and projection of TF binding motifs
- Transcription factor information
- Multiple sequence alignment
- Phylogenetic trees
- Quick search
- TF prediction server
- Help for PlantRegMap
Data Source
The deadline for species collection was Jun. 15th, 2016. 156 species (157 organisms) with public available genome sequences and 9 species with UniGene entries more than 8000 and important in economy were collected. For 156 species with genome sequences, gene sets annotated by corresponding genome projects are used. For 9 species without genome sequences, a protein dataset was integrated from UniGene EST and PlantGDB PUT for each species (see methods).
Species | Common name | Genome Anotation | UniGene | PlantGDB |
- | IKGC | - | - | |
Tausch's goatgrass | BGI | - | - | |
- | VEGI(v2.5) | - | - | |
grain amaranth | BYU | - | - | |
- | TAGP | - | - | |
pineapple | JGI(v3) | - | - | |
columbine | JGI(v3.1) | - | - | |
- | JGI(v1.1) | - | - | |
lyrate rockcress | JGI(v1.0) | - | - | |
thale cress | TAIR10 | - | - | |
alpine rockcress | MPIPBR | - | - | |
- | NCGR_PGC | - | - | |
- | NCGR_PGC | - | - | |
- | BGI | - | - | |
- | NGD | - | - | |
- | ORCAE | - | - | |
beet | TBVR(v2) | - | - | |
- | JGI(v1.2) | - | - | |
purple false brome | JGI(v3.1) | - | - | |
- | JGI(v1.1) | - | - | |
rape | Genoscope(v5) | - | - | |
- | NCBI 100 | - | - | |
field mustard | NCBI 100 | - | - | |
- | IIPG | - | - | |
false flax | CSGP | - | - | |
- | CCBR | - | - | |
- | JGI(v1.1) | - | - | |
- | JGI(v1.0) | - | - | |
chilli pepper | PEP(v1.55) | - | - | |
papaya | ASGPB | - | - | |
Chinese chestnut | THGP(v1.1) | - | - | |
Madagascar periwinkle | MPGR | - | - | |
- | JGI(v5.5) | - | - | |
- | JGI(v1.0) | - | - | |
- | NCBI 101 | - | - | |
- | ICuGI(v1) | - | - | |
- | ICGC(v1.0) | - | - | |
Valencia orange | ICGC(v1.1) | - | - | |
- | JGI(v2) | - | - | |
robusta coffee | CGSC | - | - | |
- | MELONOMICS(v3.5) | - | - | |
cucumber | JGI, V1.0 | - | - | |
Queen Anne's lace | ARS-USDA(v2.0) | - | - | |
carnation | DCA(v1.0) | - | - | |
- | Dichan(v1) | - | - | |
- | CNU(v1) | - | - | |
- | JGI(v1.0) | - | - | |
African oil palm | OG | - | - | |
tef | Tef(v3) | - | - | |
Murray red gum | ECGD | - | - | |
- | JGI(v2.0) | - | - | |
- | JGI(v1.0) | - | - | |
strawberry | kazusa(v1.1) | - | - | |
- | GDR(v1.1) | - | - | |
- | LSMU | - | - | |
soybean | Wm82.a2.v1 | - | - | |
wild soybean | TCUHK | - | - | |
- | GPGRP | - | - | |
tree cotton | BGI-A2(v1.0) | - | - | |
upland cotton | NAU-NBI(v1.1) | - | - | |
- | JGI(v2.1) | - | - | |
- | UBC | - | - | |
barley | IBSC(v1.0) | - | - | |
European hop | HOPBASE(v1.1) | - | - | |
- | Kazusa(v1.0) | - | - | |
- | Kazusa(v4.5) | - | - | |
English walnut | JHU | - | - | |
- | JGI(v1.1) | - | - | |
- | JGI(v1.1) | - | - | |
- | KFGP(v1.0) | - | - | |
- | OGE | - | - | |
- | BGI(v1.0) | - | - | |
- | Kazusa(v3.0) | - | - | |
apple | GDR(v1.0) | - | - | |
cassava | JGI(v6.1) | - | - | |
liverwort | JGI(v3.1) | - | - | |
barrel medic | Mt4.0v1 | - | - | |
- | JGI(v3.0) | - | - | |
- | JGI(v3.0) | - | - | |
spotted monkey flower | JGI(v2.0) | - | - | |
- | BU | - | - | |
- | BGI | - | - | |
- | CIRAD | - | - | |
- | CAS(v2.0) | - | - | |
- | BTI | - | - | |
wood tobacco | NCBI 100 | - | - | |
tobacco | NCBI 100 | - | - | |
- | NCBI 100 | - | - | |
holy basil | OteDB | - | - | |
- | JGI(v1.0) | - | - | |
- | OGE | - | - | |
- | OGE(v1.4) | - | - | |
- | AGI1.1 | - | - | |
- | OGE | - | - | |
long-staminate rice | BGI | - | - | |
- | OGE | - | - | |
- | OGE | - | - | |
- | OGE | - | - | |
common wild rice | OGE | - | - | |
Indian rice | RIS, Glean | - | - | |
Japanese rice | MSU(v7) | - | - | |
- | JGI(v2.0) | - | - | |
- | JGI(v2.0) | - | - | |
- | JGI(v2.0) | - | - | |
- | JGI(v2.0) | - | - | |
switchgrass | JGI(v3.1) | - | - | |
large white petunia | SGN(v1.6.2) | - | - | |
- | SGN(v1.0.1) | - | - | |
- | BGI | - | - | |
- | JGI(v1.0) | - | - | |
- | PDK(v3) | - | - | |
- | ICBR(v1.0) | - | - | |
- | COSMOSS(v3.3) | - | - | |
- | ConGenIE(v1.0) | - | - | |
- | Rutgers | - | - | |
Euphrates poplar | LZU | - | - | |
black cottonwood | JGI(v3.0) | - | - | |
Japanese apricot | BGI | - | - | |
peach | JGI(v2.1) | - | - | |
Douglas-fir | PRS(v1.0) | - | - | |
- | CPETR(v1.0) | - | - | |
jointed charlock | MSU | - | - | |
radish | RGD | - | - | |
castor bean | JCVI(v0.1) | - | - | |
purple osier | JGI(v1.0) | - | - | |
Chinese salvia | NDCTCM | - | - | |
- | JGI(v1.0) | - | - | |
beniseed | NCBI 100 | - | - | |
- | JGI(v2.2) | - | - | |
- | JGI(v1.1) | - | - | |
- | VEGI(v1) | - | - | |
tomato | ITAG(v2.3) | - | - | |
aubergine | EGD | - | - | |
- | spenn(v2.0) | - | - | |
currant tomato | CSHL | - | - | |
potato | PGSC | - | - | |
sorghum | JGI(v3.1) | - | - | |
- | JGI(v0.5) | - | - | |
spinach | TBVR(v1) | - | - | |
great duckweed | MIPS/IBIS(v2) | - | - | |
- | NCBI 100 | - | - | |
- | thellungiella(v2.0) | - | - | |
cocoa | CGD(v1.1) | - | - | |
peavine clover | JGI(v2) | - | - | |
Wheat | IWGSC(v1.0)+popseq(v31) | - | - | |
- | BGI | - | - | |
- | UGSP | - | - | |
adzuki bean | SNU(v3) | - | - | |
mung bean | SNU(v6) | - | - | |
wine grape | Genoscope | - | - | |
- | JGI(v2.1) | - | - | |
maize | MaizeSequence(AGPv3.31/5b+) | - | - | |
Chinese jujube | NCBI 100 | - | - | |
- | JGI(v2.2) | - | - | |
Japanese lawn grass | ZGD(v1.1) | - | - | |
Japanese carpet grass | ZGD(v1.0) | - | - | |
- | ZGD(v1.0) | - | - | |
peanut | - | Build #4 | 171a | |
sweet wormwood | - | Build #6 | 183a | |
sunflower | - | Build #12 | 169a | |
garden lettuce | - | Build #17 | 187a | |
white spruce | - | Build #15 | 175a | |
Sitka spruce | - | Build #16 | 183a | |
loblolly pine | - | Build #13 | 157a | |
sugarcane | - | Build #15 | 157a | |
cowpea | - | Build #4 | 167a |