Supplementary Note 1
This supplementary note covers three sets of information available as popups in EEDB.
1. Edge types and edge weights used in EdgeExpressDB.
TFBS predictions
TFBS EDGES: Evolutionarily conserved Transcription factor binding sites are predicted using MOTEVO
with a set of non-redundant matrices (combining JASPAR, TRANSFAC and a small set of de-novo motifs
trained on ChIP-chip datasets).
TFBS WEIGHTS: The weights on TFBS edges are “response values”, these are central to the FANTOM4analysis and basically say how well the expression of each LEVEL2 promoter responds to (or matches)the motif activity for that factor (eg. MYB motif activity decreases as the cells differentiate and PRTN3 aknown (and predicted) target of MYB is down-regulated, hence it has a high response weight of 14.125).
We recommend to users wishing to validate sites, response weights >1.5 are more reliable. For moredetail on TFBS prediction and motif activity please refer to the FANTOM4 manuscript text and Fig. 1(Suzuki et al. 2009).

ChIP-chip
ChIP EDGES: The FANTOM4 consortium generated chromatin immunoprecipitation on chip data for SPI1and SP1, for these factors, a peak of binding within 1kb of a promoter is considered positive evidence foran edge between these factors and the target gene. Public ChIP-chip and ChIP-seq datasets were also
incorporated, for these we relied on the primary publication’s definition of positive binding, and weinclude a PubMed link back to the corresponding citation.
ChIP WEIGHTS: The weights used here are the number of experiments this TF has been observed
binding at the target gene’s promoter (ie. a weight of 4, means it has been observed in 4 separate ChIPchip experiments).

miRNA
miRNA EDGES: miRNA to target transcript predictions were downloaded from the EIMMO prediction
server (http://www.mirz.unibas.ch/ElMMo2/). Edges are then drawn to the corresponding Entrez Gene.
miRNA WEIGHTS: Weights provided are the prediction strengths from the EIMMO software.

Perturbation
PERTURBATION EDGES: siRNA knockdown(KD) of 52 transcription factors(TF) and over-expression of 12
miRNAs was used to identify TFs and miRNAs involved in THP-1 differentiation and maintenance of theundifferentiated state. Affected genes were assessed by Illumina microarrays 48 hours post transfection.
The array data was quantile normalized and compared to negative control siRNAs and pre-miRNAs to
identify genes that are specifically perturbed in response to the TF/miRNA.
PERTURBATION WEIGHTS: The perturbation edges displayed in EEDB are stringently filtered, by log foldchange >=1/<=-1 and B-statistic >=2.5. A positive log FC means the transcript is induced upon
knockdown of the siRNA or over-expression of the miRNA. A negative log FC means the transcript isdown-regulated in response to the perturbation (eg. CD14 is strongly induced upon MYB KD and has alog FC of 6.8, whereas vitrin is strongly repressed upon MYB KD and has a log FC of -4.0).

OtherOTHER EDGES: This section contains additional nodes linked to this gene. This section includes publishedprotein-DNA edges, and is also used to manage transcripts (accession numbers), microarray probes andLevel3 promoters associated with a given gene (ie. belongs-to relationships).
For the published protein-DNA edges we include a small manuscript icon which can be clicked on andwill take the user to the corresponding PubMed citation.
OTHER WEIGHTS: Weights for this section are set to a default of 1.

Protein-protein interactions
PROTEIN-PROTEIN EDGES: The protein-protein interactions currently displayed in EEDB are fromtranscription factor – transcription factor interactions only and are harvested from a number of public
protein-protein interaction sources including DIP, BIND and HPRD (which is shown in the source).
PROTEIN-PROTEIN WEIGHTS: Weights are currently set to a default value of 1.

PUBLISHED PROTEIN DNA
PUBLISHED PROTEIN DNA EDGES: For the published protein-DNA edges we include a hyperlink to thecorresponding PubMed citation.
PUBLISHED PROTEIN DNA WEIGHT: By default set to 1.

2. CAGE defined promoters

CAGE DEFINED PROMOTERSPROMOTER LEVELS: For FANTOM4 we developed three levels to describe the relationship between
individual transcription start sites (TSS), promoters and promoter regions. Individual TSS are referred toas level 1 (L1), nearby TSSs positions whose expression profiles are the same up to measurement noiseare clustered into promoters (L2) and adjacent promoters that are within 400bp of each other arecondensed into ‘promoter regions’ (L3). For further details on promoter levels please refer to theFANTOM4 main manuscript, text and Fig. 1 (Suzuki et al. 2009).
L3

P1 corresponds to a level 3 promoter region which can contain multiple level 2 promoters (eg. P1
L2

L2and P2 ). Note: TFBS predictions are done per level3, BUT response weight is calculated for each level2 promoter

3. Explanation of the subnet viewTHE SUBNET VIEW
The subnet view allows for one to input a list of gene and/or miRNA names as nodes in a graph. Thesystem will search for all matching connecting edges within that set of nodes based on user selectableedge filters.
INTERFACE:NODE SELECTION: Users enter Entrez genes and mirbase microRNA IDs into the text box
PRIMARY EDGE TYPES: The system allows for simple logic by providing two edge sets (primary andsecondary). If only edges in set1 are selected then a simple search is performed.
SECONDARY EDGE TYPES: If edges from both sets are selected the search is performed for genes thatare connected by BOTH lines of evidence (eg. TFBS prediction in set 1 and perturbation or CHIP in set2),
this can be used to prune TFBS predictions to only those for which there is some experimental support.
EXPAND NEIGHBOURS: Warning this is currently slow. It is used to fluff out a network one extra layer(default is off).
HIDE SINGLETONS: Hides nodes that have no incoming or outgoing edges (default is on)
HIDE LEAVES: Hides nodes with only incoming edges (default is off)
LEGEND:EDGE COLOURS: BLACK – FANTOM4 Transcription factor binding site predictions and miRNA target
predictions, YELLOW – published protein-DNA edges, PURPLE – protein-protein interactions, GREEN –chip-chip(protein-DNA) edges, RED – siRNA and miRNA perturbation edges.
EDGE LINE STYLE: SOLID – Direct edges, DASHED – perturbation edges (possibly direct or indirect)
EDGE TERMINATORS: Arrowhead – activating relationships, Blunt – repressing relationships, round –bidirectional protein-protein relationships
NODE SHAPE: Round nodes are genes, hexagonal nodes are miRNAs.
NODE DIAMETER: The diameter of each node is scaled to indicate the 'dynamics' of the gene. Calculatedby mapping to log(max(detected ILMN expression)/min(detected ILMN expression)) within the timecourse. Highly dynamic nodes are larger than statically expressed nodes.
NODE COLOUR: The color of the node is mapped to a relative scale for each node between white formin(detected ILMN expression) and purple max(detected ILMN expression). If the node has nodetectable ILMN expression, the name of the node becomes red and the background is white.