Find a gene by its name Find genes
Find a gene by its name Find genes by their GO annotation Find genes by their Interpro annotation Find a molecular tool Find a clone Display the anatomical ontology for a given stage Find an anatomical territory on an embryo scheme Find Cis-reg regions by name Blast Genome browser Cis-regulatory card Gene regulation /function card Anatomical network card Clone card Expression card Anatomical structure card Article Card Find the progeny/precursors of a territory Find territories by their fates Keyword search Find neighbours of a cell Find cells by their shapes Find asymmetric cleavages Digital Differential Display Find genes expressed in a given territory Find In situ patterns linked to a gene/clone Find in situ patterns linked to a regulatory region Find coexpressed genes at a given stage Find articles related to a given gene Find articles describing the specification of a given cell fate Search articles by authors or title word Tassy et al. , Figure S 1: Navigation diagram of ANISEED
Tassy et al. , Figure S 2: ANISEED menus
A 8 -cell stage Early tailbud stage Young adult B b 8. 19 Dorsal TNC ependymal cells Dorsal posterior sensory vesicle Dorsal visceral ganglion B 7. 5 Anterior ventral primary muscle lineage Trunk ventral cells B 7. 6 Posterior endodermal strand (B 8. 11 line) Germ cell precursors (B 8. 12 line) C. intestinalis, C. savignyi, P. mammillata b 8. 19 Dorsal TNC ependymal cells Dorsal posterior sensory vesicle Dorsal visceral ganglion Posterior most secondary muscle lineage B 7. 5 Anterior ventral primary muscle lineage Trunk ventral cells Endoderm B 7. 6 Posterior endodermal strand (B 8. 11 line) Germ cell precursors (B 8. 12 line) H. roretzi, B. villosa C Tassy et al. , Figure S 3
Cleavage (64 -cell) Cleavage (76 -cell) Early Gastrula (112 -cell) Gastrula (128 -cell) Tassy et al. , Figure S 4: Three-dimensional replicas of Ciona intestinalis embryos between the 64 and 128 cell stages.
Biological name Paralogs Blast. P Orthologs Inparanoid Gene models Clones Clustering Manual annotation Gene ontology Interproscan Functional prediction Motif prediction Tassy et al. , Figure S 5: The NISEED gene annotation pipeline
Gene Exon Insulator Silencer Enhancer Basal prom. Exon Enhancer Silencer Basal Promoter: : A cis-regulatory region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. (SO: 0000167) Enhancer: A short cis-regulatory region, located away from the basal promoter and that drives a simple expression pattern. (SO: 0000165) Silencer : A cis-regulatory region, which upon binding of sequence-specific transcription factors, represses the transcription of the gene or genes it controls. (SO: 0000625) Insulator : A cis-regulatory region that when located between a cis-regulatory module (CRM; enhancer or silencer) and a gene's promoter, prevents the CRM from modulating that gene’s expression (SO: 0000627) Extended Promoter : A 5’ flanking sequence, including basal promoter and cis-regulatory modules, and showing transcriptional activity Complex Region : A genomic region with transcriptional cis-regulatory activity, which can encompass 5’ flanking, intronic and 3’ flanking regions of a gene Untested region : a genomic region which has not been experimentally tested. Usually defined as a root sequence including two or more non-overlapping elements (boxed in blue) tested in vivo. Inactive region: a genomic region which has no transcriptional cis-regulatory activity. (SO: 010001) Tassy et al. , Figure S 6: Classification of cis-regulatory sequences
4 -Cell 8 -Cell 16 -Cell 32 -Cell 64 -Cell 112 -Cell A 6. 1 A 5. 1 A 4. 1 A 6. 2 A 7. 5 A 7. 6 A 7. 7 A 7. 8 A 6. 3 A 5. 2 A 6. 4 A 3 a 7. 9 a 7. 10 a 7. 11 a 6. 5 a 5. 3 a 6. 6 a 4. 2 a 7. 13 a 7. 14 a 6. 7 a 5. 4 AB A 8. 11 A 8. 12 a 8. 17 a 8. 18 a 8. 19 a 8. 20 a 8. 25 a 8. 26 a 6. 8 B 6. 1 B 5. 1 B 4. 1 B 6. 2 B 6. 3 B 5. 2 B 3 B 6. 4 b 6. 5 b 5. 3 b 4. 2 b 6. 6 b 6. 7 b 5. 4 B 8. 5 B 8. 6 B 7. 3 B 7. 4 b 6. 8 B 7. 5 B 7. 6 B 7. 7 B 7. 8 b 7. 9 b 7. 10 b 7. 11 b 7. 12 b 7. 13 b 7. 14 b 7. 15 b 7. 16 b 8. 19 b 8. 20 b 8. 21 b 8. 22 b 8. 25 b 8. 26 Weakly unequal cleavage (index >15%) Markedly unequal cleavage (index >25%) Very strongly unequal cleavage (index >50%) Tassy et al. , Figure S 7: Unequal cleavages between fertilization and the onset of gastrulation
Molecular queries Gene Ontology (Localization) Digital Differential Display (Expression) Extracellular proteins (815 gene models) Expressed at cleavage stages (348 gene models) Query integration by ID In Situ (Spatial expression) Anatomical queries Correct spatial expression (2 gene models) Biometry Vegetal neighbors at the 16 -cell stage of mother of a 6. 5 (2 cell pairs) Lineage Mother of a 6. 5 cell pair at the 16 -cell stage (2 cells) (Distance) Tassy et al. Figure S 8: In silico identification of the anterior neural inducer by sequential querying of heterogeneous data.
140 Interactions from Imai et al. (2006) "ANISEED inferred interactions" Number of interactions 120 100 80 60 40 20 Late tailbud Mid tailbud Early tailbud Mid neurula Late gastrula Mid gastrula 112 -cell stage 64 -cell stage Late 32 -cell stage 16 -cell stage 0 Developmental stage when interactions were analyzed. Tassy et al. , Figure S 9: Automatic inference of regulatory interactions significantly extends the Ciona developmental Gene Regulatory Network.
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