Diapositive 1

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Find a gene by its name
Find Cis-reg regions by name
Blast
Keyword search
Digital Differential Display
Find genes by their GO annotation
Genome browser
Cis-regulatory card
Find genes expressed in a given territory
Find genes by their Interpro annotation
Find In situ patterns linked to a gene/clone
Gene card
Gene regulation /function card
Find a molecular tool
Find in situ patterns linked to a regulatory
region
Anatomical network card
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Clone card
Display the anatomical ontology for a given stage
Find coexpressed genes at a given stage
Expression card
Anatomical structure card
Find articles related to a given gene
Find an anatomical territory on an embryo scheme
Article Card
Find articles describing the specification of a
given cell fate
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Find territories by their fates
Tassy et al., Figure S1 Navigation diagram of
ANISEED
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(No Transcript)
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Tassy et al., Figure S3
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Tassy et al., Figure S4 Three-dimensional
replicas of Ciona intestinalis embryos between
the 64 and 128 cell stages.
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Manual annotation
Functional prediction
Biological name
Gene ontology
BlastP
Paralogs
Orthologs
Inparanoid
Interproscan
Gene models
Clones
Motif prediction
Clustering
Tassy et al., Figure S5The NISEED gene
annotation pipeline
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Gene
Exon
Exon
Insulator
Enhancer
Basal prom.
Silencer
Silencer
Enhancer

• Basal Promoter A cis-regulatory region
  composed of the TSS(s) and binding sites for
  TF_complexes of the basal transcription
  machinery. (SO0000167)
• Enhancer A short cis-regulatory region, located
  away from the basal promoter and that drives a
  simple expression pattern. (SO0000165)
• Silencer A cis-regulatory region, which upon
  binding of sequence-specific transcription
  factors, represses the transcription of the gene
  or genes it controls. (SO0000625)
• 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 genes
  expression (SO0000627)
• 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.

Tassy et al., Figure S6 Classification of
cis-regulatory sequences
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4-Cell
16-Cell
32-Cell
64-Cell
112-Cell
8-Cell
A6.1
A5.1
A6.2
A7.5
A4.1
A6.3
A8.11
A7.6
A8.12
A5.2
A7.7
A6.4
A7.8
a 8.17
A3
a7.9
a 8.18
a6.5
a 8.19
a7.10
a 8.20
a5.3
a7.11
a6.6
a7.12
a 8.25
a4.2
a7.13
a 8.26
a6.7
a7.14
a5.4
a6.8
AB
B6.1
B5.1
B 8.5
B7.3
B 8.6
B6.2
B7.4
B4.1
B7.5
B6.3
B7.6
B5.2
B7.7
B6.4
B7.8
B3
b7.9
b6.5
b 8.19
b7.10
b 8.20
b5.3
b 8.21
b 8.22
b7.11
b6.6
b7.12
b 8.25
b4.2
b 8.26
b7.13
b6.7
b7.14
b5.4
b7.15
b6.8
b7.16
Weakly unequal cleavage (index gt15)
Markedly unequal cleavage (index gt25)
Very strongly unequal cleavage (index gt50)
Tassy et al., Figure S7 Unequal cleavages
between fertilization and the onset of
gastrulation
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Extracellular proteins (815 gene models)
Gene Ontology (Localization)
Molecular queries
Digital Differential Display (Expression)
Expressed at cleavage stages (348 gene models)
Query integration by ID
In Situ (Spatial expression)
Correct spatial expression (2 gene models)
Vegetal neighbors at the 16-cell stage of mother
of a6.5 (2 cell pairs)
Biometry (Distance)
Anatomical queries
Mother of a6.5 cell pair at the 16-cell stage (2
cells)
Lineage
Tassy et al. Figure S8 In silico identification
of the anterior neural inducer by sequential
querying of heterogeneous data.
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Number of interactions
Developmental stage when interactions were
analyzed.
Tassy et al., Figure S9 Automatic inference of
regulatory interactions significantly extends the
Ciona developmental Gene Regulatory Network.