Phatr_bicluster_0128 Residual: 0.39
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_0128 0.39 Phaeodactylum tricornutum
Displaying 1 - 32 of 32
PHATRDRAFT_10100 magnesium-subunit h (PLN03241)

PHATRDRAFT_10100 - magnesium-subunit h (PLN03241)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10100
PHATRDRAFT_10546 ribokinase (ribokinase)

PHATRDRAFT_10546 - ribokinase (ribokinase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10546
PHATRDRAFT_12544 (PcbC)

PHATRDRAFT_12544 - (PcbC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12544
PHATRDRAFT_13053 xpa binding protein 2

PHATRDRAFT_13053 - xpa binding protein 2

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13053
PHATRDRAFT_13835 ylm1_schpo tpr repeat-containing protein (TPR)

PHATRDRAFT_13835 - ylm1_schpo tpr repeat-containing protein (TPR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13835
PHATRDRAFT_15479 calcium-dependent protein kinase (S_TKc)

PHATRDRAFT_15479 - calcium-dependent protein kinase (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15479
PHATRDRAFT_16827 unusual protein kinase (AarF)

PHATRDRAFT_16827 - unusual protein kinase (AarF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16827
PHATRDRAFT_21039 rna-binding protein (RRM_SF superfamily)

PHATRDRAFT_21039 - rna-binding protein (RRM_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21039
PHATRDRAFT_22821 phosphoglycerate bisphosphoglycerate mutase family protein (HP_PGM_like)

PHATRDRAFT_22821 - phosphoglycerate bisphosphoglycerate mutase family protein (HP_PGM_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22821
PHATRDRAFT_24935 rh26_orysj dead-box atp-dependent rna helicase 26 (DEXDc superfamily)

PHATRDRAFT_24935 - rh26_orysj dead-box atp-dependent rna helicase 26 (DEXDc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24935
PHATRDRAFT_30609

PHATRDRAFT_30609 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30609
PHATRDRAFT_35397

PHATRDRAFT_35397 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35397
PHATRDRAFT_35669 nadph-dependent fmn and fad containing oxidoreductase-likepartial

PHATRDRAFT_35669 - nadph-dependent fmn and fad containing oxidoreductase-likepartial

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35669
PHATRDRAFT_37403

PHATRDRAFT_37403 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37403
PHATRDRAFT_37417 cytochrome c biogenesisccb2 (DUF2930 superfamily)

PHATRDRAFT_37417 - cytochrome c biogenesisccb2 (DUF2930 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37417
PHATRDRAFT_38343

PHATRDRAFT_38343 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38343
PHATRDRAFT_39646

PHATRDRAFT_39646 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39646
PHATRDRAFT_40279

PHATRDRAFT_40279 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40279
PHATRDRAFT_43158

PHATRDRAFT_43158 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43158
PHATRDRAFT_44196 copia protein (gag-int-pol protein)

PHATRDRAFT_44196 - copia protein (gag-int-pol protein)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44196
PHATRDRAFT_45259

PHATRDRAFT_45259 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45259
PHATRDRAFT_45944

PHATRDRAFT_45944 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45944
PHATRDRAFT_46270 (START_2)

PHATRDRAFT_46270 - (START_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46270
PHATRDRAFT_46431 sensor histidine kinase with a pas domain

PHATRDRAFT_46431 - sensor histidine kinase with a pas domain

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46431
PHATRDRAFT_46975

PHATRDRAFT_46975 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46975
PHATRDRAFT_47240

PHATRDRAFT_47240 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47240
PHATRDRAFT_48221

PHATRDRAFT_47717 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47717
PHATRDRAFT_49342 alpha beta hydrolase fold (Hydrolase_4 superfamily)

PHATRDRAFT_48221 - alpha beta hydrolase fold (Hydrolase_4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48221
PHATRDRAFT_54756 (Spond_N superfamily)

PHATRDRAFT_49342 - (Spond_N superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49342
PHATRDRAFT_6586 phosphatidate cytidylyltransferase (CdsA)

PHATRDRAFT_54756 - phosphatidate cytidylyltransferase (CdsA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54756
PHATRDRAFT_7679 gas41 (gliomas 41) (YEATS)

PHATRDRAFT_6586 - gas41 (gliomas 41) (YEATS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6586

PHATRDRAFT_7679 - fibrinolytic enzyme (Tryp_SPc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7679
GO ID Go Term p-value q-value Cluster
GO:0006014 D-ribose metabolism 0.00345508 1 Phatr_bicluster_0128
GO:0009058 biosynthesis 0.0753046 1 Phatr_bicluster_0128
GO:0006396 RNA processing 0.0929544 1 Phatr_bicluster_0128
GO:0006468 protein amino acid phosphorylation 0.262204 1 Phatr_bicluster_0128
GO:0006355 regulation of transcription, DNA-dependent 0.322627 1 Phatr_bicluster_0128
GO:0006508 proteolysis and peptidolysis 0.328797 1 Phatr_bicluster_0128
GO:0008152 metabolism 0.410263 1 Phatr_bicluster_0128
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