Phatr_bicluster_0013 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_0013 0.38 Phaeodactylum tricornutum
Displaying 1 - 25 of 25
PHATRDRAFT_12243 peptide methionine sulfoxide reductase1 (PMSR superfamily)

PHATRDRAFT_12243 - peptide methionine sulfoxide reductase1 (PMSR superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12243
PHATRDRAFT_13078 permease

PHATRDRAFT_13078 - permease

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13078
PHATRDRAFT_22353 solute carrier family 9 (sodium hydrogen exchanger)member 8 (NhaP)

PHATRDRAFT_22353 - solute carrier family 9 (sodium hydrogen exchanger)member 8 (NhaP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22353
PHATRDRAFT_2527 tbc1 domainmember 13 (TBC)

PHATRDRAFT_2527 - tbc1 domainmember 13 (TBC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2527
PHATRDRAFT_29042 nucleotide-sugar transporter family protein

PHATRDRAFT_29042 - nucleotide-sugar transporter family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29042
PHATRDRAFT_29793 methyltransferase family member 1 (RF_mod_PrmC)

PHATRDRAFT_29793 - methyltransferase family member 1 (RF_mod_PrmC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29793
PHATRDRAFT_31322 (EFh)

PHATRDRAFT_31322 - (EFh)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31322
PHATRDRAFT_33304 small nuclear ribonucleoprotein d2-like protein (Sm_D2)

PHATRDRAFT_33304 - small nuclear ribonucleoprotein d2-like protein (Sm_D2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33304
PHATRDRAFT_33535 abcperiplasmic binding component (Phosphonate-bd superfamily)

PHATRDRAFT_33535 - abcperiplasmic binding component (Phosphonate-bd superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33535
PHATRDRAFT_35862 (DUF2256)

PHATRDRAFT_35862 - (DUF2256)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35862
PHATRDRAFT_36381

PHATRDRAFT_36381 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36381
PHATRDRAFT_39074 (PUB)

PHATRDRAFT_39074 - (PUB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39074
PHATRDRAFT_39656

PHATRDRAFT_39656 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39656
PHATRDRAFT_41349 (DnaJ)

PHATRDRAFT_41349 - (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41349
PHATRDRAFT_42708 (Condensation superfamily)

PHATRDRAFT_42708 - (Condensation superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42708
PHATRDRAFT_44479 strictosidine synthase family protein (Str_synth superfamily)

PHATRDRAFT_44479 - strictosidine synthase family protein (Str_synth superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44479
PHATRDRAFT_44658 non muscle myosin

PHATRDRAFT_44658 - non muscle myosin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44658
PHATRDRAFT_45794 (EFh)

PHATRDRAFT_45794 - (EFh)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45794
PHATRDRAFT_47823

PHATRDRAFT_47823 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47823
PHATRDRAFT_47844

PHATRDRAFT_47844 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47844
PHATRDRAFT_47894 metallo cofactor biosynthesis protein (COG0535)

PHATRDRAFT_47894 - metallo cofactor biosynthesis protein (COG0535)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47894
PHATRDRAFT_48888 cell wall surface anchor family protein

PHATRDRAFT_48888 - cell wall surface anchor family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48888
PHATRDRAFT_49109

PHATRDRAFT_49109 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49109
PHATRDRAFT_52110 alanine-glyoxylate aminotransferase 2-like 1 (OAT_like)

PHATRDRAFT_52110 - alanine-glyoxylate aminotransferase 2-like 1 (OAT_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52110
PHATRDRAFT_55087 membrane protein containing duf1625 (DUF1625)

PHATRDRAFT_55087 - membrane protein containing duf1625 (DUF1625)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55087
GO ID Go Term p-value q-value Cluster
GO:0006479 protein amino acid methylation 0.00542673 1 Phatr_bicluster_0013
GO:0007160 cell-matrix adhesion 0.00813004 1 Phatr_bicluster_0013
GO:0006885 regulation of pH 0.0215467 1 Phatr_bicluster_0013
GO:0006814 sodium ion transport 0.0295173 1 Phatr_bicluster_0013
GO:0007155 cell adhesion 0.0347981 1 Phatr_bicluster_0013
GO:0008643 carbohydrate transport 0.0426705 1 Phatr_bicluster_0013
GO:0006306 DNA methylation 0.0530761 1 Phatr_bicluster_0013
GO:0006397 mRNA processing 0.0608128 1 Phatr_bicluster_0013
GO:0009058 biosynthesis 0.115816 1 Phatr_bicluster_0013
GO:0006464 protein modification 0.158622 1 Phatr_bicluster_0013
Log in to post comments