Phatr_bicluster_0001 Residual: 0.41
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_0001 0.41 Phaeodactylum tricornutum
Displaying 1 - 46 of 46
PHATRDRAFT_1199 leucine-rich repeat family protein (AMN1 superfamily)

PHATRDRAFT_1199 - leucine-rich repeat family protein (AMN1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1199
PHATRDRAFT_15815 vacuolar-type h+-pyrophosphatase (hppA)

PHATRDRAFT_15815 - vacuolar-type h+-pyrophosphatase (hppA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15815
PHATRDRAFT_16987 dead deah box helicase domain protein (DEXDc superfamily)

PHATRDRAFT_16987 - dead deah box helicase domain protein (DEXDc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16987
PHATRDRAFT_1784 cytosolic imp-gmp specific 5- (5_nucleotid superfamily)

PHATRDRAFT_1784 - cytosolic imp-gmp specific 5- (5_nucleotid superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1784
PHATRDRAFT_23365 3-oxoacidtransferase 1 (CoA_trans superfamily)

PHATRDRAFT_23365 - 3-oxoacidtransferase 1 (CoA_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23365
PHATRDRAFT_30786 xylose isomerase-like tim barrel (PRK05474)

PHATRDRAFT_30786 - xylose isomerase-like tim barrel (PRK05474)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30786
PHATRDRAFT_43237

PHATRDRAFT_43237 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43237
PHATRDRAFT_43441

PHATRDRAFT_43441 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43441
PHATRDRAFT_43794

PHATRDRAFT_43794 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43794
PHATRDRAFT_43872

PHATRDRAFT_43872 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43872
PHATRDRAFT_43959 heat shockprotein (DnaJ)

PHATRDRAFT_43959 - heat shockprotein (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43959
PHATRDRAFT_44009 (Lactonase)

PHATRDRAFT_44009 - (Lactonase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44009
PHATRDRAFT_44049 erythroid differentiation-related factor 1-like protein

PHATRDRAFT_44049 - erythroid differentiation-related factor 1-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44049
PHATRDRAFT_44229 (ATG11 superfamily)

PHATRDRAFT_44229 - (ATG11 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44229
PHATRDRAFT_45953 emb2473 (embryo defective 2473) gtp binding calcium ion binding (Ras_like_GTPase superfamily)

PHATRDRAFT_45953 - emb2473 (embryo defective 2473) gtp binding calcium ion binding (Ras_like_GTPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45953
PHATRDRAFT_47553 (COG4278 superfamily)

PHATRDRAFT_47553 - (COG4278 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47553
PHATRDRAFT_47689 signal transduction histidine kinase (BaeS)

PHATRDRAFT_47689 - signal transduction histidine kinase (BaeS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47689
PHATRDRAFT_47858

PHATRDRAFT_47858 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47858
PHATRDRAFT_47865 ycii-related protein (YCII superfamily)

PHATRDRAFT_47865 - ycii-related protein (YCII superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47865
PHATRDRAFT_47911

PHATRDRAFT_47911 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47911
PHATRDRAFT_47912 pa and ring finger domain protein (RING)

PHATRDRAFT_47912 - pa and ring finger domain protein (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47912
PHATRDRAFT_47933 at5g51450 mfg13_16 (RING)

PHATRDRAFT_47933 - at5g51450 mfg13_16 (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47933
PHATRDRAFT_47973

PHATRDRAFT_47973 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47973
PHATRDRAFT_48027

PHATRDRAFT_48027 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48027
PHATRDRAFT_48047

PHATRDRAFT_48047 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48047
PHATRDRAFT_48163 ankyrin repeat (ANK)

PHATRDRAFT_48163 - ankyrin repeat (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48163
PHATRDRAFT_48166 (DUF179)

PHATRDRAFT_48166 - (DUF179)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48166
PHATRDRAFT_48195

PHATRDRAFT_48195 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48195
PHATRDRAFT_48527

PHATRDRAFT_48527 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48527
PHATRDRAFT_48594

PHATRDRAFT_48594 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48594
PHATRDRAFT_48634 ring-type e3 ubiquitin ligase

PHATRDRAFT_48634 - ring-type e3 ubiquitin ligase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48634
PHATRDRAFT_49067

PHATRDRAFT_49067 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49067
PHATRDRAFT_49110

PHATRDRAFT_49110 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49110
PHATRDRAFT_49119 alpha beta hydrolase fold (Abhydrolase_6)

PHATRDRAFT_49119 - alpha beta hydrolase fold (Abhydrolase_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49119
PHATRDRAFT_49286

PHATRDRAFT_49286 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49286
PHATRDRAFT_49618 stress response protein

PHATRDRAFT_49618 - stress response protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49618
PHATRDRAFT_49620 hsf-type dna-binding domain containing protein (HSF_DNA-bind)

PHATRDRAFT_49620 - hsf-type dna-binding domain containing protein (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49620
PHATRDRAFT_49722

PHATRDRAFT_49722 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49722
PHATRDRAFT_49785 protein-l-isoaspartate (d-aspartate) o-methyltransferase domain containing 2

PHATRDRAFT_49785 - protein-l-isoaspartate (d-aspartate) o-methyltransferase domain containing 2

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49785
PHATRDRAFT_50049 programmed cell death 4a (MA3)

PHATRDRAFT_50049 - programmed cell death 4a (MA3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50049
PHATRDRAFT_50130 at3g05760 f10a16_5 (ZnF_U1)

PHATRDRAFT_50130 - at3g05760 f10a16_5 (ZnF_U1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50130
PHATRDRAFT_50224

PHATRDRAFT_50224 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50224
PHATRDRAFT_50347 nitrate reductase (Cyt-b5)

PHATRDRAFT_50347 - nitrate reductase (Cyt-b5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50347
PHATRDRAFT_50491

PHATRDRAFT_50491 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50491
PHATRDRAFT_50523 carbohydrate-binding protein

PHATRDRAFT_50523 - carbohydrate-binding protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50523
PHATRDRAFT_54477 atp citrate lyase isoform 2 isoform 13 (PLN02522)

PHATRDRAFT_54477 - atp citrate lyase isoform 2 isoform 13 (PLN02522)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54477
GO ID Go Term p-value q-value Cluster
GO:0000160 two-component signal transduction system (phosphorelay) 0.0084651 1 Phatr_bicluster_0001
GO:0001539 ciliary or flagellar motility 0.0162159 1 Phatr_bicluster_0001
GO:0016567 protein ubiquitination 0.0572963 1 Phatr_bicluster_0001
GO:0016310 phosphorylation 0.0735532 1 Phatr_bicluster_0001
GO:0015992 proton transport 0.0735532 1 Phatr_bicluster_0001
GO:0006810 transport 0.0823394 1 Phatr_bicluster_0001
GO:0007264 small GTPase mediated signal transduction 0.108364 1 Phatr_bicluster_0001
GO:0006355 regulation of transcription, DNA-dependent 0.112841 1 Phatr_bicluster_0001
GO:0015031 protein transport 0.155936 1 Phatr_bicluster_0001
GO:0007165 signal transduction 0.227048 1 Phatr_bicluster_0001
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