Phatr_bicluster_0066 Residual: 0.37
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_0066 0.37 Phaeodactylum tricornutum
Displaying 1 - 30 of 30
PHATRDRAFT_10747 flavin reductase-related (SDR_a5)

PHATRDRAFT_10747 - flavin reductase-related (SDR_a5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10747
PHATRDRAFT_11792 psab translation factor (DUF1092 superfamily)

PHATRDRAFT_11792 - psab translation factor (DUF1092 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11792
PHATRDRAFT_12097 zinc finger (c3hc4-type ring finger) family protein (zinc_ribbon_6)

PHATRDRAFT_12097 - zinc finger (c3hc4-type ring finger) family protein (zinc_ribbon_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12097
PHATRDRAFT_12106 ku70-binding family protein (Peptidase_M76 superfamily)

PHATRDRAFT_12106 - ku70-binding family protein (Peptidase_M76 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12106
PHATRDRAFT_2957 histone acetyltransferase (Bromodomain superfamily)

PHATRDRAFT_2957 - histone acetyltransferase (Bromodomain superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2957
PHATRDRAFT_31822 nadph oxidoreductase (NADB_Rossmann superfamily)

PHATRDRAFT_31822 - nadph oxidoreductase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31822
PHATRDRAFT_31834

PHATRDRAFT_31834 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31834
PHATRDRAFT_31835

PHATRDRAFT_31835 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31835
PHATRDRAFT_34859 glyoxalase bleomycin resistance protein dioxygenase (Glo_EDI_BRP_like_6)

PHATRDRAFT_34859 - glyoxalase bleomycin resistance protein dioxygenase (Glo_EDI_BRP_like_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34859
PHATRDRAFT_35733 (NADB_Rossmann superfamily)

PHATRDRAFT_35627 - (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35627
PHATRDRAFT_36008 (DUF1632 superfamily)

PHATRDRAFT_35733 - (DUF1632 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35733
PHATRDRAFT_36009 type i secretion target repeat

PHATRDRAFT_36008 - type i secretion target repeat

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36008
PHATRDRAFT_36269 type i secretion target repeat

PHATRDRAFT_36009 - type i secretion target repeat

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36009
PHATRDRAFT_37941

PHATRDRAFT_36269 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36269
PHATRDRAFT_38426

PHATRDRAFT_37941 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37941
PHATRDRAFT_38705

PHATRDRAFT_38426 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38426
PHATRDRAFT_41106 (PDZ superfamily)

PHATRDRAFT_38705 - (PDZ superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38705
PHATRDRAFT_43236 germination protein

PHATRDRAFT_41106 - germination protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41106
PHATRDRAFT_43417

PHATRDRAFT_41493 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41493
PHATRDRAFT_45294 (TPR_12)

PHATRDRAFT_43236 - (TPR_12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43236
PHATRDRAFT_45346 endonuclease iii (ENDO3c)

PHATRDRAFT_43417 - endonuclease iii (ENDO3c)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43417
PHATRDRAFT_45366 sepiapterin reductase (NADB_Rossmann superfamily)

PHATRDRAFT_45294 - sepiapterin reductase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45294
PHATRDRAFT_45757 traf-type zinc finger family protein

PHATRDRAFT_45346 - traf-type zinc finger family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45346
PHATRDRAFT_45789

PHATRDRAFT_45366 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45366
PHATRDRAFT_46375 alkaline phosphatase d domain protein (MPP_PhoD)

PHATRDRAFT_45757 - alkaline phosphatase d domain protein (MPP_PhoD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45757
PHATRDRAFT_46642 auxin efflux carrier family protein (Mem_trans superfamily)

PHATRDRAFT_45789 - auxin efflux carrier family protein (Mem_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45789
PHATRDRAFT_8934 (DUF303 superfamily)

PHATRDRAFT_46375 - (DUF303 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46375
PHATRDRAFT_9664 cg14021-isoform b isoform 2

PHATRDRAFT_46642 - cg14021-isoform b isoform 2

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46642

PHATRDRAFT_8934 - proteintkl group (STYKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8934

PHATRDRAFT_9664 - cathepsin z (Peptidase_C1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9664
GO ID Go Term p-value q-value Cluster
GO:0016567 protein ubiquitination 0.00618161 1 Phatr_bicluster_0066
GO:0006614 SRP-dependent cotranslational protein-membrane targeting 0.00861852 1 Phatr_bicluster_0066
GO:0006508 proteolysis and peptidolysis 0.053216 1 Phatr_bicluster_0066
GO:0006468 protein amino acid phosphorylation 0.262204 1 Phatr_bicluster_0066
GO:0008152 metabolism 0.410263 1 Phatr_bicluster_0066
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