Phatr_bicluster_0152 Residual: 0.19
Phaeodactylum tricornutum

Module Page Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.
Title Residual Model version Organism
Phatr_bicluster_0152 0.19 Phaeodactylum tricornutum
Displaying 1 - 17 of 17
PHATRDRAFT_11126 aspartyl glutamyl-trna(asn gln) amidotransferase subunit b (GatB)

PHATRDRAFT_11126 - aspartyl glutamyl-trna(asn gln) amidotransferase subunit b (GatB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11126
PHATRDRAFT_13581 dna topoisomerase ii (PLN03128)

PHATRDRAFT_13581 - dna topoisomerase ii (PLN03128)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13581
PHATRDRAFT_14917 methionyl-trna formyltransferase (PLN02285)

PHATRDRAFT_14917 - methionyl-trna formyltransferase (PLN02285)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14917
PHATRDRAFT_24739 (gltB)

PHATRDRAFT_24739 - (gltB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24739
PHATRDRAFT_27166 spermidine putrescine abc transporter atp-binding subunit (PGDH_like_3)

PHATRDRAFT_27166 - spermidine putrescine abc transporter atp-binding subunit (PGDH_like_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27166
PHATRDRAFT_31994 chloroplast fructose--bisphosphatase (FBPase)

PHATRDRAFT_31994 - chloroplast fructose--bisphosphatase (FBPase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31994
PHATRDRAFT_33016 (BolA)

PHATRDRAFT_33016 - (BolA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33016
PHATRDRAFT_4025 dihydrodipicolinate reductase family protein (PLN02775)

PHATRDRAFT_4025 - dihydrodipicolinate reductase family protein (PLN02775)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4025
PHATRDRAFT_44459 translation initiation factor (IF4E superfamily)

PHATRDRAFT_44459 - translation initiation factor (IF4E superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44459
PHATRDRAFT_44833 efgm_arath probable elongation factormitochondrial precursor (EF-G)

PHATRDRAFT_44833 - efgm_arath probable elongation factormitochondrial precursor (EF-G)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44833
PHATRDRAFT_46012 (U3snoRNP10)

PHATRDRAFT_46012 - (U3snoRNP10)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46012
PHATRDRAFT_47056 tpr domain protein

PHATRDRAFT_47056 - tpr domain protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47056
PHATRDRAFT_47067 phosphoribosylglycinamidephosphoribosylglycinamidephosphoribosylaminoimidazole synthetase (PRK00885)

PHATRDRAFT_47067 - phosphoribosylglycinamidephosphoribosylglycinamidephosphoribosylaminoimidazole synthetase (PRK00885)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47067
PHATRDRAFT_48338 caf1 family (CAF1 superfamily)

PHATRDRAFT_48338 - caf1 family (CAF1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48338
PHATRDRAFT_48410 brain protein 16 (DUF383 superfamily)

PHATRDRAFT_48410 - brain protein 16 (DUF383 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48410
PHATRDRAFT_50034 emb2742 (embryo defective 2742) ctp synthase (PLN02327)

PHATRDRAFT_50034 - emb2742 (embryo defective 2742) ctp synthase (PLN02327)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50034
PHATRDRAFT_8270 rna-binding region rnp-1 (RRM_SF superfamily)

PHATRDRAFT_8270 - rna-binding region rnp-1 (RRM_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8270
GO ID Go Term p-value q-value Cluster
GO:0016481 negative regulation of transcription 0.00887241 1 Phatr_bicluster_0152
GO:0009113 purine base biosynthesis 0.00887241 1 Phatr_bicluster_0152
GO:0006221 pyrimidine nucleotide biosynthesis 0.00887241 1 Phatr_bicluster_0152
GO:0009089 lysine biosynthesis via diaminopimelate 0.0132807 1 Phatr_bicluster_0152
GO:0009058 biosynthesis 0.0165059 1 Phatr_bicluster_0152
GO:0006189 'de novo' IMP biosynthesis 0.0220418 1 Phatr_bicluster_0152
GO:0006537 glutamate biosynthesis 0.0220418 1 Phatr_bicluster_0152
GO:0006564 L-serine biosynthesis 0.0350457 1 Phatr_bicluster_0152
GO:0006265 DNA topological change 0.0393439 1 Phatr_bicluster_0152
GO:0006259 DNA metabolism 0.0521304 1 Phatr_bicluster_0152
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