Phatr_bicluster_0072 Residual: 0.33
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_0072 0.33 Phaeodactylum tricornutum
Displaying 1 - 29 of 29
PHATRDRAFT_10539 atpk19 atpk2 (arabidopsis thaliana serine threonine protein kinasearabidopsis thaliana serine threonine protein kinase 2) kinase (STKc_AGC)

PHATRDRAFT_10539 - atpk19 atpk2 (arabidopsis thaliana serine threonine protein kinasearabidopsis thaliana serine threonine protein kinase 2) kinase (STKc_AGC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10539
PHATRDRAFT_13864 lsm (like-sm) domain-containing protein (Sm_D3)

PHATRDRAFT_13864 - lsm (like-sm) domain-containing protein (Sm_D3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13864
PHATRDRAFT_15516 myb3r-4 (c-myb-like transcription factor 3r-myb domain protein 3r-4) dna binding transcription factor (SANT)

PHATRDRAFT_15516 - myb3r-4 (c-myb-like transcription factor 3r-myb domain protein 3r-4) dna binding transcription factor (SANT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15516
PHATRDRAFT_15555 (PRK08566)

PHATRDRAFT_15555 - (PRK08566)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15555
PHATRDRAFT_16615 polyprenyl synthetase (Trans_IPPS_HT)

PHATRDRAFT_16615 - polyprenyl synthetase (Trans_IPPS_HT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16615
PHATRDRAFT_22703 exosome component 10 (DnaQ_like_exo superfamily)

PHATRDRAFT_22703 - exosome component 10 (DnaQ_like_exo superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22703
PHATRDRAFT_23253 mate efflux family protein (MATE_DinF_like)

PHATRDRAFT_23253 - mate efflux family protein (MATE_DinF_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23253
PHATRDRAFT_23908 oxoglutarate malate translocator (Mito_carr)

PHATRDRAFT_23908 - oxoglutarate malate translocator (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23908
PHATRDRAFT_38064

PHATRDRAFT_38064 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38064
PHATRDRAFT_38110

PHATRDRAFT_38110 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38110
PHATRDRAFT_38867

PHATRDRAFT_38867 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38867
PHATRDRAFT_40433 solute carrier family 34 (sodium phosphate)member 2 (2a58)

PHATRDRAFT_40433 - solute carrier family 34 (sodium phosphate)member 2 (2a58)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40433
PHATRDRAFT_40779 multidrug efflux mfs permease (MFS)

PHATRDRAFT_40779 - multidrug efflux mfs permease (MFS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40779
PHATRDRAFT_40930 cytochrome c heme (Cyto_heme_lyase superfamily)

PHATRDRAFT_40930 - cytochrome c heme (Cyto_heme_lyase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40930
PHATRDRAFT_42373 aldo keto reductase (Aldo_ket_red)

PHATRDRAFT_42373 - aldo keto reductase (Aldo_ket_red)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42373
PHATRDRAFT_4342 mitochondrial carrier (Mito_carr)

PHATRDRAFT_4342 - mitochondrial carrier (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4342
PHATRDRAFT_45597 effluxfamily transporter (FUSC_2)

PHATRDRAFT_45597 - effluxfamily transporter (FUSC_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45597
PHATRDRAFT_47598

PHATRDRAFT_47598 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47598
PHATRDRAFT_47754 ring-h2 zinc finger (RING)

PHATRDRAFT_47754 - ring-h2 zinc finger (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47754
PHATRDRAFT_47771

PHATRDRAFT_47771 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47771
PHATRDRAFT_48508 signal recognition particle

PHATRDRAFT_48508 - signal recognition particle

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48508
PHATRDRAFT_48750 cop-ii coat subunit

PHATRDRAFT_48750 - cop-ii coat subunit

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48750
PHATRDRAFT_49061

PHATRDRAFT_49061 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49061
PHATRDRAFT_49155

PHATRDRAFT_49155 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49155
PHATRDRAFT_49641 (LabA_like)

PHATRDRAFT_49641 - (LabA_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49641
PHATRDRAFT_49767 (ZnF_UBR1)

PHATRDRAFT_49767 - (ZnF_UBR1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49767
PHATRDRAFT_50084 glutathione peroxidase (Thioredoxin_like superfamily)

PHATRDRAFT_50084 - glutathione peroxidase (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50084
PHATRDRAFT_50304

PHATRDRAFT_50304 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50304
PHATRDRAFT_50408 mitochondrial inner membrane transporter ymc1 (Mito_carr)

PHATRDRAFT_50408 - mitochondrial inner membrane transporter ymc1 (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50408
GO ID Go Term p-value q-value Cluster
GO:0006366 transcription from RNA polymerase II promoter 0.00419857 1 Phatr_bicluster_0072
GO:0006810 transport 0.00703653 1 Phatr_bicluster_0072
GO:0006855 multidrug transport 0.0166949 1 Phatr_bicluster_0072
GO:0006817 phosphate transport 0.0290436 1 Phatr_bicluster_0072
GO:0008299 isoprenoid biosynthesis 0.0371948 1 Phatr_bicluster_0072
GO:0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.0412462 1 Phatr_bicluster_0072
GO:0006350 transcription 0.0847655 1 Phatr_bicluster_0072
GO:0006397 mRNA processing 0.0924756 1 Phatr_bicluster_0072
GO:0006512 ubiquitin cycle 0.148383 1 Phatr_bicluster_0072
GO:0006468 protein amino acid phosphorylation 0.161086 1 Phatr_bicluster_0072
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