Phatr_bicluster_0065 Residual: 0.38
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_0065 0.38 Phaeodactylum tricornutum
Displaying 1 - 28 of 28
PHATRDRAFT_14536 small chain (clathrin associated complex) family member (aps-3) (APS2)

PHATRDRAFT_14536 - small chain (clathrin associated complex) family member (aps-3) (APS2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14536
PHATRDRAFT_16490 novel proteindiaphorase(cytochrome b-5 reductase) (cyt_b5_reduct_like)

PHATRDRAFT_16490 - novel proteindiaphorase(cytochrome b-5 reductase) (cyt_b5_reduct_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16490
PHATRDRAFT_22064 mob1-like protein (Mob1_phocein superfamily)

PHATRDRAFT_22064 - mob1-like protein (Mob1_phocein superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22064
PHATRDRAFT_2648 cell cycle switch protein (WD40 superfamily)

PHATRDRAFT_2648 - cell cycle switch protein (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2648
PHATRDRAFT_3262 glycerol-3-phosphate acyltransferase (LPLAT superfamily)

PHATRDRAFT_3262 - glycerol-3-phosphate acyltransferase (LPLAT superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3262
PHATRDRAFT_34715 pirin domain protein (COG1741)

PHATRDRAFT_34715 - pirin domain protein (COG1741)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34715
PHATRDRAFT_34844

PHATRDRAFT_34844 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34844
PHATRDRAFT_37958

PHATRDRAFT_37958 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37958
PHATRDRAFT_38713 cysteine peptidase active site-type peptidasecatalyticibonuclease h fold

PHATRDRAFT_38713 - cysteine peptidase active site-type peptidasecatalyticibonuclease h fold

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38713
PHATRDRAFT_40774 (ABM)

PHATRDRAFT_40774 - (ABM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40774
PHATRDRAFT_42912

PHATRDRAFT_42912 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42912
PHATRDRAFT_42944 (DUF3591 superfamily)

PHATRDRAFT_42944 - (DUF3591 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42944
PHATRDRAFT_43665 integral membrane protein (PI-PLCc_At5g67130_like)

PHATRDRAFT_43665 - integral membrane protein (PI-PLCc_At5g67130_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43665
PHATRDRAFT_43963

PHATRDRAFT_43963 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43963
PHATRDRAFT_47496 (DUF605)

PHATRDRAFT_47496 - (DUF605)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47496
PHATRDRAFT_47567

PHATRDRAFT_47567 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47567
PHATRDRAFT_47892 methyltransferase type 11

PHATRDRAFT_47892 - methyltransferase type 11

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47892
PHATRDRAFT_48358 tetratricopeptide tpr_2 repeat protein (TPR_12)

PHATRDRAFT_48358 - tetratricopeptide tpr_2 repeat protein (TPR_12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48358
PHATRDRAFT_48727 sdrf_staepserine-aspartate repeat-containing protein f precursor

PHATRDRAFT_48727 - sdrf_staepserine-aspartate repeat-containing protein f precursor

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48727
PHATRDRAFT_48778 acyl--binding protein (ACBP superfamily)

PHATRDRAFT_48778 - acyl--binding protein (ACBP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48778
PHATRDRAFT_48783 snf1 like protein kinase (S_TKc)

PHATRDRAFT_48783 - snf1 like protein kinase (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48783
PHATRDRAFT_49213

PHATRDRAFT_49213 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49213
PHATRDRAFT_50333 sulfate transporter family protein (SUL1)

PHATRDRAFT_50333 - sulfate transporter family protein (SUL1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50333
PHATRDRAFT_50435 (PHA03247)

PHATRDRAFT_50435 - (PHA03247)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50435
PHATRDRAFT_50576

PHATRDRAFT_50576 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50576
PHATRDRAFT_51174 atp-bindingsub-family fmember 1 (Uup)

PHATRDRAFT_51174 - atp-bindingsub-family fmember 1 (Uup)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51174
PHATRDRAFT_54915 cysk2_schpo cysteine synthase 2 (o-acetylserine sulfhydrylase 2) (o-acetylserine-lyase 2) (csase 2) (CBS_like)

PHATRDRAFT_54915 - cysk2_schpo cysteine synthase 2 (o-acetylserine sulfhydrylase 2) (o-acetylserine-lyase 2) (csase 2) (CBS_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54915
PHATRDRAFT_8683 msra_sollcpeptide methionine sulfoxide reductase (protein-methionine-s-oxide reductase) (peptide-methionine-s-oxide reductase) (peptide metreductase) (fruit-ripening protein e4) (PMSR)

PHATRDRAFT_8683 - msra_sollcpeptide methionine sulfoxide reductase (protein-methionine-s-oxide reductase) (peptide-methionine-s-oxide reductase) (peptide metreductase) (fruit-ripening protein e4) (PMSR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8683
GO ID Go Term p-value q-value Cluster
GO:0006118 electron transport 0.33492 1 Phatr_bicluster_0065
GO:0006886 intracellular protein transport 0.0671851 1 Phatr_bicluster_0065
GO:0007242 intracellular signaling cascade 0.0704402 1 Phatr_bicluster_0065
GO:0008152 metabolism 0.410263 1 Phatr_bicluster_0065
GO:0006468 protein amino acid phosphorylation 0.262204 1 Phatr_bicluster_0065
GO:0006464 protein modification 0.104035 1 Phatr_bicluster_0065
GO:0007165 signal transduction 0.0785354 1 Phatr_bicluster_0065
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