Phatr_bicluster_0054 Residual: 0.38
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_0054 0.38 Phaeodactylum tricornutum
Displaying 1 - 27 of 27
PHATRDRAFT_10438 zeta-carotene desaturase (HpnE)

PHATRDRAFT_10438 - zeta-carotene desaturase (HpnE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10438
PHATRDRAFT_14449 proteasome subunit beta type 1 (Ntn_hydrolase superfamily)

PHATRDRAFT_14449 - proteasome subunit beta type 1 (Ntn_hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14449
PHATRDRAFT_14856 ribosomal large subunit pseudouridylate synthase (RsuA)

PHATRDRAFT_14856 - ribosomal large subunit pseudouridylate synthase (RsuA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14856
PHATRDRAFT_15338 smad nuclear interacting protein (FHA)

PHATRDRAFT_15338 - smad nuclear interacting protein (FHA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15338
PHATRDRAFT_2032 nitrate transporter (2A0108)

PHATRDRAFT_2032 - nitrate transporter (2A0108)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2032
PHATRDRAFT_31234 cog0398: uncharacterized conserved protein (COG0398)

PHATRDRAFT_31234 - cog0398: uncharacterized conserved protein (COG0398)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31234
PHATRDRAFT_33208

PHATRDRAFT_33208 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33208
PHATRDRAFT_38929

PHATRDRAFT_38929 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38929
PHATRDRAFT_40791

PHATRDRAFT_40791 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40791
PHATRDRAFT_41411

PHATRDRAFT_41411 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41411
PHATRDRAFT_42897

PHATRDRAFT_42897 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42897
PHATRDRAFT_44799 had-superfamily hydrolase subfamilyvariant 1 and 3 (COG1011)

PHATRDRAFT_44799 - had-superfamily hydrolase subfamilyvariant 1 and 3 (COG1011)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44799
PHATRDRAFT_46342

PHATRDRAFT_46342 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46342
PHATRDRAFT_47361 exodeoxyribonuclease iii xth (Ape1-like_AP-endo)

PHATRDRAFT_47361 - exodeoxyribonuclease iii xth (Ape1-like_AP-endo)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47361
PHATRDRAFT_47730 recombination and dna strand exchange inhibitor protein (ABC_ATPase superfamily)

PHATRDRAFT_47730 - recombination and dna strand exchange inhibitor protein (ABC_ATPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47730
PHATRDRAFT_48256

PHATRDRAFT_48256 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48256
PHATRDRAFT_48538 vacuolar transporter chaperone (CYTH-like_Pase superfamily)

PHATRDRAFT_48538 - vacuolar transporter chaperone (CYTH-like_Pase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48538
PHATRDRAFT_48708

PHATRDRAFT_48708 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48708
PHATRDRAFT_49309

PHATRDRAFT_49309 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49309
PHATRDRAFT_49502 tricarboxylate carrier

PHATRDRAFT_49502 - tricarboxylate carrier

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49502
PHATRDRAFT_49871

PHATRDRAFT_49871 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49871
PHATRDRAFT_50328 golden2-like transcription factor

PHATRDRAFT_50328 - golden2-like transcription factor

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50328
PHATRDRAFT_5156 prolyl 4-hydroxylase alpha subunit (P4Hc)

PHATRDRAFT_5156 - prolyl 4-hydroxylase alpha subunit (P4Hc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5156
PHATRDRAFT_52367 cadmium-transporting atpase-like protein (ZntA)

PHATRDRAFT_52367 - cadmium-transporting atpase-like protein (ZntA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52367
PHATRDRAFT_54598 enhanced disease susceptibility 5 (MATE_like superfamily)

PHATRDRAFT_54598 - enhanced disease susceptibility 5 (MATE_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54598
PHATRDRAFT_5811 (Hydrolase)

PHATRDRAFT_5811 - (Hydrolase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5811
PHATRDRAFT_6402 af361805_1at1g56180 f14g9_20

PHATRDRAFT_6402 - af361805_1at1g56180 f14g9_20

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6402
GO ID Go Term p-value q-value Cluster
GO:0006298 mismatch repair 0.0118036 1 Phatr_bicluster_0054
GO:0006259 DNA metabolism 0.0234852 1 Phatr_bicluster_0054
GO:0006281 DNA repair 0.0652904 1 Phatr_bicluster_0054
GO:0019538 protein metabolism 0.069012 1 Phatr_bicluster_0054
GO:0006511 ubiquitin-dependent protein catabolism 0.0855993 1 Phatr_bicluster_0054
GO:0006396 RNA processing 0.105521 1 Phatr_bicluster_0054
GO:0008152 metabolism 0.109996 1 Phatr_bicluster_0054
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