Phatr_bicluster_0087 Residual: 0.27
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_0087 0.27 Phaeodactylum tricornutum
Displaying 1 - 28 of 28
PHATRDRAFT_10677 copper-exporting atpase (ZntA)

PHATRDRAFT_10677 - copper-exporting atpase (ZntA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10677
PHATRDRAFT_1358 cg1814-isoform c (5_nucleotid superfamily)

PHATRDRAFT_1358 - cg1814-isoform c (5_nucleotid superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1358
PHATRDRAFT_15063 sec14 cytosolic factor family protein phosphoglyceride transfer family protein (SEC14)

PHATRDRAFT_15063 - sec14 cytosolic factor family protein phosphoglyceride transfer family protein (SEC14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15063
PHATRDRAFT_15917 cystathionine gamma-lyase (CGS_like)

PHATRDRAFT_15917 - cystathionine gamma-lyase (CGS_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15917
PHATRDRAFT_32014 mfs family transporter: sugar (MFS_1)

PHATRDRAFT_32014 - mfs family transporter: sugar (MFS_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32014
PHATRDRAFT_32314 short-chain dehydrogenase reductase sdr (NADB_Rossmann superfamily)

PHATRDRAFT_32314 - short-chain dehydrogenase reductase sdr (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32314
PHATRDRAFT_35984 s-adenosylmethionine transporter (Mito_carr)

PHATRDRAFT_35984 - s-adenosylmethionine transporter (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35984
PHATRDRAFT_36021

PHATRDRAFT_36021 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36021
PHATRDRAFT_36196 nudix hydrolase (Nudix_Hydrolase superfamily)

PHATRDRAFT_36196 - nudix hydrolase (Nudix_Hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36196
PHATRDRAFT_36356 had-superfamilysubfamily iia (NagD)

PHATRDRAFT_36356 - had-superfamilysubfamily iia (NagD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36356
PHATRDRAFT_37547 ankyrin repeat (ANK)

PHATRDRAFT_37547 - ankyrin repeat (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37547
PHATRDRAFT_42616

PHATRDRAFT_42616 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42616
PHATRDRAFT_43088 mgc81853 protein (Vac14_Fab1_bd)

PHATRDRAFT_43088 - mgc81853 protein (Vac14_Fab1_bd)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43088
PHATRDRAFT_43238

PHATRDRAFT_43238 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43238
PHATRDRAFT_43894

PHATRDRAFT_43894 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43894
PHATRDRAFT_44225 af271290_1 gamma-tubulin (PLN00222)

PHATRDRAFT_44225 - af271290_1 gamma-tubulin (PLN00222)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44225
PHATRDRAFT_44370 and mbr-like protein (TspO_MBR superfamily)

PHATRDRAFT_44370 - and mbr-like protein (TspO_MBR superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44370
PHATRDRAFT_44480 mgc82690 protein (MFS)

PHATRDRAFT_44480 - mgc82690 protein (MFS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44480
PHATRDRAFT_44747 rma1 (ring finger protein with membrane anchor 1) protein binding ubiquitin-protein ligase zinc ion binding (RING)

PHATRDRAFT_44747 - rma1 (ring finger protein with membrane anchor 1) protein binding ubiquitin-protein ligase zinc ion binding (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44747
PHATRDRAFT_44924

PHATRDRAFT_44924 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44924
PHATRDRAFT_45174 alkaline phosphatase d domain protein (MPP_PhoD)

PHATRDRAFT_45174 - alkaline phosphatase d domain protein (MPP_PhoD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45174
PHATRDRAFT_45175

PHATRDRAFT_45175 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45175
PHATRDRAFT_46430

PHATRDRAFT_46430 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46430
PHATRDRAFT_46478

PHATRDRAFT_46478 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46478
PHATRDRAFT_46667 thump domain containing 3 (AdoMet_MTases superfamily)

PHATRDRAFT_46667 - thump domain containing 3 (AdoMet_MTases superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46667
PHATRDRAFT_48656 domain containing 7 (zf-DHHC)

PHATRDRAFT_48656 - domain containing 7 (zf-DHHC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48656
PHATRDRAFT_48797 loc564023 protein (DUF1295 superfamily)

PHATRDRAFT_48797 - loc564023 protein (DUF1295 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48797
PHATRDRAFT_9115 mgc116538 protein (AdoMet_MTases superfamily)

PHATRDRAFT_9115 - mgc116538 protein (AdoMet_MTases superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9115
GO ID Go Term p-value q-value Cluster
GO:0007018 microtubule-based movement 0.00457016 1 Phatr_bicluster_0087
GO:0051258 protein polymerization 0.0171775 1 Phatr_bicluster_0087
GO:0006810 transport 0.025594 1 Phatr_bicluster_0087
GO:0015992 proton transport 0.0474084 1 Phatr_bicluster_0087
GO:0030001 metal ion transport 0.0540081 1 Phatr_bicluster_0087
GO:0008152 metabolism 0.0758904 1 Phatr_bicluster_0087
GO:0006520 amino acid metabolism 0.0799844 1 Phatr_bicluster_0087
GO:0006812 cation transport 0.0895536 1 Phatr_bicluster_0087
GO:0016567 protein ubiquitination 0.222443 1 Phatr_bicluster_0087
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