Dataset:

Metazoan protein sequences were collected from NCBI RefSeq database (Release 60, 17 species) and ensembl (Release 72, 60 species).


Maternal factors:

Maternal factors were expressed in unfertilized eggs, and gradually reduced as time goes on. In order to reduce the search space of developmentally important genes, we only focused on those specifically expressed genes in egg stages, whose expression value 8 times than the mean value of others.


Gene ID:

For genes have NCBI RefSeq sequences, we used NCBI RefSeq 'GeneID' as the gene's ID, for genes only have ensembl sequences, we used ensembl gene ID as the gene's ID.


Gene annotation:

InterPro annotation was conducted by InterProScan with all programes: including FPrintScan, HMMPfam, HMMSmart, ProfileScan, PatternScan, SuperFamily, SignalPHMM, TMHMM, Gene3D and so on.

Pfam annotation was conducted independently by hmmer with evalue 1e-3.

Gene ontology annotation was carried out by BLAST protein sequences against Uniprot/Swiss-Prot protein databse (evalue 1e-10). GO terms hit at least half of the top 10 target proteins were adopted.


Ortholog & Paralog:

Orthologs were predicted using BLASTP bidirectional best hit with evalue 1e-20; Paralogs were predicted with BLAST identity 70% & evalue 1e-50.


Gene expression profiles

Gene expression were collected from NCBI GEO, and normalized by GCRMA with a log2 transformed value. The data list used could be found from here.


Browse transcription factors of a species:

Click the Species menu, choose an interest species.


Browse transcription factors of a species by taxonomic class:

Click the Browse menu, choose an interest taxonomic class and species on the left panel, the details will be displayed inthe right panel.


Browse transcription factors by family:

Click the Family menu, choose an interest family.


Browse maternal factors of Homo sapiens and Mus musculus:

Choose the Browse or Maternal menu, click the corresponding pictures or links.


Browse transcription factors & maternal factors of a special development ontology:

Choose the Ontology menu, click the links of an interest development level and term, and all child nodes (is_a & part_of) will be searched.


Taxonomic Groups:

TAXID Organism Kingdom Phylum Class Order Family Genus Species
8090 Oryzias latipes Animalia Chordata Actinopterygii Beloniformes Adrianichthyidae Oryzias O.latipes
8083 Xiphophorus maculatus Animalia Chordata Actinopterygii Cyprinodontiformes Poeciliidae Xiphophorus X.maculatus
69293 Gasterosteus aculeatus Animalia Chordata Actinopterygii Gasterosteiformes Gasterosteidae Gasterosteus G.aculeatus
8128 Oreochromis niloticus Animalia Chordata Actinopterygii Perciformes Cichlidae Oreochromis O.niloticus
31033 Takifugu rubripes Animalia Chordata Actinopterygii Tetraodontiformes Tetraodontidae Takifugu T.rubripes
99883 Tetraodon nigroviridis Animalia Chordata Actinopterygii Tetraodontiformes Tetraodontidae Tetraodon T.nigroviridis
8049 Gadus morhua Animalia Chordata Actinopterygii Gadiformes Gadidae Gadus G.morhua
7955 Danio rerio Animalia Chordata Actinopterygii Cypriniformes Cyprinidae Danio D.rerio
8364 Xenopus tropicalis Animalia Chordata Amphibia Anura Pipidae Xenopus X.tropicalis
7897 Latimeria chalumnae Animalia Chordata Sarcopterygii Coelacanthiformes Latimeriidae Latimeria L.chalumnae
28377 Anolis carolinensis Animalia Chordata Reptilia Squamata Polychrotidae Anolis A.carolinensis
9813 Procavia capensis Animalia Chordata Mammalia Hyracoidea Procaviidae Procavia P.capensis
9785 Loxodonta africana Animalia Chordata Mammalia Proboscidea Elephantidae Loxodonta L.africana
9371 Echinops telfairi Animalia Chordata Mammalia Afrosoricida Tenrecidae Echinops E.telfairi
9986 Oryctolagus cuniculus Animalia Chordata Mammalia Lagomorpha Leporidae Oryctolagus O.cuniculus
9978 Ochotona princeps Animalia Chordata Mammalia Lagomorpha Ochotonidae Ochotona O.princeps
10141 Cavia porcellus Animalia Chordata Mammalia Rodentia Caviidae Cavia C.porcellus
10020 Dipodomys ordii Animalia Chordata Mammalia Rodentia Heteromyidae Dipodomys D.ordii
10029 Cricetulus griseus Animalia Chordata Mammalia Rodentia Cricetidae Cricetulus C.griseus
10090 Mus musculus Animalia Chordata Mammalia Rodentia Muridae Mus M.musculus
10116 Rattus norvegicus Animalia Chordata Mammalia Rodentia Muridae Rattus R.norvegicus
43179 Ictidomys tridecemlineatus Animalia Chordata Mammalia Rodentia Sciuridae Ictidomys I.tridecemlineatus
9544 Macaca mulatta Animalia Chordata Mammalia Primates Cercopithecidae Macaca M.mulatta
9555 Papio anubis Animalia Chordata Mammalia Primates Cercopithecidae Papio P.anubis
9595 Gorilla gorilla Animalia Chordata Mammalia Primates Hominidae Gorilla G.gorilla
9606 Homo sapiens Animalia Chordata Mammalia Primates Hominidae Homo H.sapiens
9598 Pan troglodytes Animalia Chordata Mammalia Primates Hominidae Pan P.troglodytes
9597 Pan paniscus Animalia Chordata Mammalia Primates Hominidae Pan P.paniscus
9601 Pongo abelii Animalia Chordata Mammalia Primates Hominidae Pongo P.abelii
61853 Nomascus leucogenys Animalia Chordata Mammalia Primates Hylobatidae Nomascus N.leucogenys
9483 Callithrix jacchus Animalia Chordata Mammalia Primates Callitrichidae Callithrix C.jacchus
39432 Saimiri boliviensis Animalia Chordata Mammalia Primates Cebidae Saimiri S.boliviensis
9478 Tarsius syrichta Animalia Chordata Mammalia Primates Tarsiidae Carlito T.syrichta
30608 Microcebus murinus Animalia Chordata Mammalia Primates Cheirogaleidae Microcebus M.murinus
30611 Otolemur garnettii Animalia Chordata Mammalia Primates Galagidae Otolemur O.garnettii
37347 Tupaia belangeri Animalia Chordata Mammalia Scandentia Tupaiidae Tupaia T.belangeri
9615 Canis familiaris Animalia Chordata Mammalia Carnivora Canidae Canis C.lupus
9669 Mustela putorius furo Animalia Chordata Mammalia Carnivora Mustelidae Mustela M.putorius
9646 Ailuropoda melanoleuca Animalia Chordata Mammalia Carnivora Ursidae Ailuropoda A.melanoleuca
9685 Felis catus Animalia Chordata Mammalia Carnivora Felidae Felis F.catus
9739 Tursiops truncatus Animalia Chordata Mammalia Cetacea Delphinidae Tursiops T.truncatus
9913 Bos taurus Animalia Chordata Mammalia Artiodactyla Bovidae Bos B.taurus
9823 Sus scrofa Animalia Chordata Mammalia Artiodactyla Suidae Sus S.scrofa
30538 Vicugna pacos Animalia Chordata Mammalia Artiodactyla Camelidae Vicugna V.pacos
132908 Pteropus vampyrus Animalia Chordata Mammalia Chiroptera Pteropodidae Pteropus P.vampyrus
59463 Myotis lucifugus Animalia Chordata Mammalia Chiroptera Vespertilionidae Myotis M.lucifugus
9365 Erinaceus europaeus Animalia Chordata Mammalia Erinaceomorpha Erinaceidae Erinaceus E.europaeus
42254 Sorex araneus Animalia Chordata Mammalia Soricomorpha Soricidae Sorex S.araneus
9796 Equus caballus Animalia Chordata Mammalia Perissodactyla Equidae Equus E.ferus
9361 Dasypus novemcinctus Animalia Chordata Mammalia Cingulata Dasypodidae Dasypus D.novemcinctus
9358 Choloepus hoffmanni Animalia Chordata Mammalia Pilosa Megalonychidae Choloepus C.hoffmanni
9305 Sarcophilus harrisii Animalia Chordata Mammalia Dasyuromorphia Dasyuridae arcophilus S.harrisii
13616 Monodelphis domestica Animalia Chordata Mammalia Didelphimorphia Didelphidae Monodelphis M.domestica
9315 Macropus eugenii Animalia Chordata Mammalia Diprotodontia Macropodidae Macropus M.eugenii
9258 Ornithorhynchus anatinus Animalia Chordata Mammalia Monotremata Ornithorhynchidae Ornithorhynchus O.anatinus
9103 Meleagris gallopavo Animalia Chordata Aves Galliformes Phasianidae Meleagris M.gallopavo
9031 Gallus gallus Animalia Chordata Aves Galliformes Phasianidae Gallus G.gallus
59729 Taeniopygia guttata Animalia Chordata Aves Passeriformes Estrildidae Taeniopygia T.guttata
13735 Pelodiscus sinensis Animalia Chordata Sauropsida Testudines Trionychidae Pelodiscus P.sinensis
7757 Petromyzon marinus Animalia Chordata Petromyzontida Petromyzontiformes Petromyzontidae Petromyzon P.marinus
34765 Oikopleura dioica Animalia Chordata Appendicularia Copelata Oikopleuridae Oikopleura O.dioica
7719 Ciona intestinalis Animalia Chordata Ascidiacea Enterogona Cionidae Ciona C.intestinalis
51511 Ciona savignyi Animalia Chordata Ascidiacea Enterogona Cionidae Ciona C.savignyi
254849 Halocynthia aurantium Animalia Chordata Ascidiacea Pleurogona Pyuridae Halocynthia H.aurantium
7729 Halocynthia roretzi Animalia Chordata Ascidiacea Pleurogona Pyuridae Halocynthia H.roretzi
6085 Hydra magnipapillata Animalia Cnidaria Hydrozoa Anthomedusae Hydridae Hydra H.magnipapillata
34638 Metaseiulus occidentalis Animalia Arthropoda Arachnida Mesostigmata Phytoseiidae Metaseiulus M.occidentalis
7070 Tribolium castaneum Animalia Arthropoda Insecta Coleoptera Tenebrionidae Tribolium T.castaneum
7227 Drosophila melanogaster Animalia Arthropoda Insecta Diptera Drosophilidae Drosophila D.melanogaster
7463 Apis florea Animalia Arthropoda Insecta Hymenoptera Apidae Apis A.florea
7460 Apis mellifera Animalia Arthropoda Insecta Hymenoptera Apidae Apis A.mellifera
30195 Bombus terrestris Animalia Arthropoda Insecta Hymenoptera Apidae Bombus B.terrestris
132113 Bombus impatiens Animalia Arthropoda Insecta Hymenoptera Apidae Bombus B.impatiens
143995 Megachile rotundata Animalia Arthropoda Insecta Hymenoptera Megachilidae Megachile M.rotundata
7425 Nasonia vitripennis Animalia Arthropoda Insecta Hymenoptera Pteromalidae Nasonia N.vitripennis
7029 Acyrthosiphon pisum Animalia Arthropoda Insecta Hemiptera Aphididae Acyrthosiphon A.pisum
6239 Caenorhabditis elegans Animalia Nematoda Chromadorea Rhabditida Rhabditidae Caenorhabditis C.elegans
7668 Strongylocentrotus purpuratus Animalia Echinodermata Echinoidea Echinoida Strongylocentrotidae Strongylocentrotus S.purpuratus
10224 Saccoglossus kowalevskii Animalia Hemichordata Enteropneusta Enteropneusta Harrimaniidae Saccoglossus S.kowalevskii
400682 Amphimedon queenslandica Animalia Porifera Demospongiae Haplosclerida Niphatidae Amphimedon A.queenslandica

Known transcription factor families:

Pfam acc Pfam ID Pfam description GO ID
PF00046 Homeobox Homeobox domain GO:0003700
PF00104 Hormone_recep Ligand-binding domain of nuclear hormone receptor GO:0003700
PF00105 zf-C4 Zinc finger, C4 type (two domains) GO:0003700
PF00157 Pou Pou domain - N-terminal to homeobox domain GO:0003700
PF00170 bZIP_1 bZIP transcription factor GO:0003700
PF00172 Zn_clus Fungal Zn(2)-Cys(6) binuclear cluster domain GO:0000981
PF00178 Ets Ets-domain GO:0003700
PF00250 Fork_head Fork head domain GO:0003700
PF00320 GATA GATA zinc finger GO:0003700
PF00447 HSF_DNA-bind HSF-type DNA-binding GO:0003700
PF00554 RHD Rel homology domain (RHD) GO:0003700
PF00853 Runt Runt domain GO:0003700
PF00859 CTF_NFI Runt domain GO:0003700
PF00907 T-box T-box GO:0003700
PF01017 STAT_alpha STAT protein, all-alpha domain GO:0003700
PF01056 Myc_N Myc amino-terminal region GO:0003700
PF01166 TSC22 TSC-22/dip/bun family GO:0003700
PF01285 TEA TEA/ATTS domain family GO:0003700
PF01422 zf-NF-X1 NF-X1 type zinc finger GO:0003700
PF01530 zf-C2HC Zinc finger, C2HC type GO:0003700
PF02023 SCAN SCAN domain GO:0003700
PF02045 CBFB_NFYA CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B GO:0003700
PF02200 STE STE like transcription factor GO:0003700
PF02319 E2F_TDP E2F/DP family winged-helix DNA-binding domain GO:0003700
PF02864 STAT_bind STAT protein, DNA binding domain GO:0003700
PF02865 STAT_int STAT protein, protein interaction domain GO:0003700
PF03529 TF_Otx Otx1 transcription factor GO:0003700
PF03792 PBC PBC domain GO:0003700
PF04621 ETS_PEA3_N PEA3 subfamily ETS-domain transcription factor N terminal domain GO:0003700
PF06546 Vert_HS_TF Vertebrate heat shock transcription factor GO:0003700
PF06621 SIM_C Single-minded protein C-terminus GO:0003700
PF07531 TAFH NHR1 homology to TAF GO:0003700
PF07716 bZIP_2 Basic region leucine zipper GO:0003700
PF09270 BTD Beta-trefoil DNA-binding domain GO:0000982
PF09271 LAG1-DNAbind LAG1, DNA binding GO:0003700
PF10401 IRF-3 Interferon-regulatory factor 3 GO:0003700
PF12162 STAT1_TAZ2bind STAT1 TAZ2 binding domain GO:0003700