Phatr_bicluster_0115 Residual: 0.43
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_0115 0.43 Phaeodactylum tricornutum
Displaying 1 - 30 of 30
PHATRDRAFT_10881 ammonium transporter-like protein amt1 (Ammonium_transp superfamily)

PHATRDRAFT_10881 - ammonium transporter-like protein amt1 (Ammonium_transp superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10881
PHATRDRAFT_11318 3-hydroxyisobutyrate dehydrogenase (MmsB)

PHATRDRAFT_11318 - 3-hydroxyisobutyrate dehydrogenase (MmsB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11318
PHATRDRAFT_12171 ferredoxin thioredoxin reductase beta chain (FeThRed_B)

PHATRDRAFT_12171 - ferredoxin thioredoxin reductase beta chain (FeThRed_B)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12171
PHATRDRAFT_12731 proteasome beta 3 subunit (Ntn_hydrolase superfamily)

PHATRDRAFT_12731 - proteasome beta 3 subunit (Ntn_hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12731
PHATRDRAFT_13232 mgc115247 protein (PLN02681)

PHATRDRAFT_13232 - mgc115247 protein (PLN02681)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13232
PHATRDRAFT_28009 rh58_orysjdead-box atp-dependent rna helicasechloroplast precursor (SrmB)

PHATRDRAFT_25184 - rh58_orysjdead-box atp-dependent rna helicasechloroplast precursor (SrmB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25184
PHATRDRAFT_32572 steroid 5alpha-reductase-like protein (Steroid_dh superfamily)

PHATRDRAFT_28009 - steroid 5alpha-reductase-like protein (Steroid_dh superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28009
PHATRDRAFT_32738

PHATRDRAFT_32572 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32572
PHATRDRAFT_32970

PHATRDRAFT_32738 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32738
PHATRDRAFT_34556

PHATRDRAFT_32970 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32970
PHATRDRAFT_34846

PHATRDRAFT_34556 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34556
PHATRDRAFT_35198

PHATRDRAFT_34846 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34846
PHATRDRAFT_35620 (PhyH superfamily)

PHATRDRAFT_35198 - (PhyH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35198
PHATRDRAFT_43051

PHATRDRAFT_35620 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35620
PHATRDRAFT_43128 stress response regulator hfs transcription (HSF_DNA-bind)

PHATRDRAFT_43051 - stress response regulator hfs transcription (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43051
PHATRDRAFT_43405

PHATRDRAFT_43128 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43128
PHATRDRAFT_43513 (Bestrophin superfamily)

PHATRDRAFT_43405 - (Bestrophin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43405
PHATRDRAFT_43621

PHATRDRAFT_43513 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43513
PHATRDRAFT_43766

PHATRDRAFT_43621 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43621
PHATRDRAFT_44921 phosphoribulokinase uridine kinase familyexpressed (NK superfamily)

PHATRDRAFT_43766 - phosphoribulokinase uridine kinase familyexpressed (NK superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43766
PHATRDRAFT_45974

PHATRDRAFT_44921 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44921
PHATRDRAFT_46351 solute carrier familymember 3 (Aa_trans superfamily)

PHATRDRAFT_45974 - solute carrier familymember 3 (Aa_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45974
PHATRDRAFT_46716 lipopolysaccharide core biosynthesis protein (CAP10 superfamily)

PHATRDRAFT_46351 - lipopolysaccharide core biosynthesis protein (CAP10 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46351
PHATRDRAFT_46813 phytanoyl-dioxygenasefamily protein (PhyH superfamily)

PHATRDRAFT_46716 - phytanoyl-dioxygenasefamily protein (PhyH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46716
PHATRDRAFT_47149 f-box familyexpressed

PHATRDRAFT_46813 - f-box familyexpressed

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46813
PHATRDRAFT_47334 (Med7 superfamily)

PHATRDRAFT_47149 - (Med7 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47149
PHATRDRAFT_48658 bromodomain containing protein (Bromodomain)

PHATRDRAFT_47334 - bromodomain containing protein (Bromodomain)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47334
PHATRDRAFT_48695 dopamine beta-monooxygenase n-terminal domain-containing (Cyt_b561_FRRS1_like)

PHATRDRAFT_48658 - dopamine beta-monooxygenase n-terminal domain-containing (Cyt_b561_FRRS1_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48658
PHATRDRAFT_55080

PHATRDRAFT_48695 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48695

PHATRDRAFT_55080 - dentin sialophosphoprotein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55080
GO ID Go Term p-value q-value Cluster
GO:0006562 proline catabolism 0.00444115 1 Phatr_bicluster_0115
GO:0006537 glutamate biosynthesis 0.01107 1 Phatr_bicluster_0115
GO:0006098 pentose-phosphate shunt 0.0132709 1 Phatr_bicluster_0115
GO:0006865 amino acid transport 0.0606018 1 Phatr_bicluster_0115
GO:0009058 biosynthesis 0.095782 1 Phatr_bicluster_0115
GO:0006511 ubiquitin-dependent protein catabolism 0.095782 1 Phatr_bicluster_0115
GO:0006810 transport 0.352949 1 Phatr_bicluster_0115
GO:0006355 regulation of transcription, DNA-dependent 0.394049 1 Phatr_bicluster_0115
GO:0006118 electron transport 0.408154 1 Phatr_bicluster_0115
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