Phatr_bicluster_0248 Residual: 0.29
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_0248 0.29 Phaeodactylum tricornutum
Displaying 1 - 31 of 31
PHATRDRAFT_12292 ribosomal protein l33 (rpmG)

PHATRDRAFT_12292 - ribosomal protein l33 (rpmG)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12292
PHATRDRAFT_12378 subfamilymember 9 (DnaJ)

PHATRDRAFT_12378 - subfamilymember 9 (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12378
PHATRDRAFT_12921 alm beta-like (S1_like superfamily)

PHATRDRAFT_12921 - alm beta-like (S1_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12921
PHATRDRAFT_13160 farnesyl diphosphate farnesyl transferase 1 (Trans_IPPS_HH)

PHATRDRAFT_13160 - farnesyl diphosphate farnesyl transferase 1 (Trans_IPPS_HH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13160
PHATRDRAFT_13167 solute carrier family 35 (UAA)

PHATRDRAFT_13167 - solute carrier family 35 (UAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13167
PHATRDRAFT_18036 dnaj domain (DnaJ)

PHATRDRAFT_18036 - dnaj domain (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18036
PHATRDRAFT_20120 solute carrier family 35 (udp-n-acetylglucosamine (udp-c) transporter)memberisoform cra_b (Nuc_sug_transp)

PHATRDRAFT_20120 - solute carrier family 35 (udp-n-acetylglucosamine (udp-c) transporter)memberisoform cra_b (Nuc_sug_transp)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20120
PHATRDRAFT_20508 long chain polyunsaturated fatty acid elongation (ELO)

PHATRDRAFT_20508 - long chain polyunsaturated fatty acid elongation (ELO)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20508
PHATRDRAFT_21275 (Abhydrolase_5)

PHATRDRAFT_21275 - (Abhydrolase_5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21275
PHATRDRAFT_27735 gmp synthase (PLN02347)

PHATRDRAFT_27735 - gmp synthase (PLN02347)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27735
PHATRDRAFT_28551 dna-dependent atpase snf2h (PLN03142)

PHATRDRAFT_28551 - dna-dependent atpase snf2h (PLN03142)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28551
PHATRDRAFT_31662 mono- or diacylglycerol acyltransferase (LPLAT superfamily)

PHATRDRAFT_31662 - mono- or diacylglycerol acyltransferase (LPLAT superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31662
PHATRDRAFT_31927 peroxisomal protein pex19 family protein (Pex19 superfamily)

PHATRDRAFT_31927 - peroxisomal protein pex19 family protein (Pex19 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31927
PHATRDRAFT_41030

PHATRDRAFT_41030 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41030
PHATRDRAFT_41875 3-bisphosphate nucleotidase (FIG superfamily)

PHATRDRAFT_41875 - 3-bisphosphate nucleotidase (FIG superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41875
PHATRDRAFT_42673 sec23_ustma protein transport protein sec23 (PLN00162)

PHATRDRAFT_42673 - sec23_ustma protein transport protein sec23 (PLN00162)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42673
PHATRDRAFT_42721 conserved protein (Gly_transf_sug superfamily)

PHATRDRAFT_42721 - conserved protein (Gly_transf_sug superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42721
PHATRDRAFT_43690

PHATRDRAFT_43690 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43690
PHATRDRAFT_43774 formin 2 (Nup54 superfamily)

PHATRDRAFT_43774 - formin 2 (Nup54 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43774
PHATRDRAFT_44312 (SMC_prok_B)

PHATRDRAFT_44312 - (SMC_prok_B)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44312
PHATRDRAFT_44505 aspartyl asparaginyl beta- (Asp_Arg_Hydrox superfamily)

PHATRDRAFT_44505 - aspartyl asparaginyl beta- (Asp_Arg_Hydrox superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44505
PHATRDRAFT_44547 ankyrin repeat (Pho88 superfamily)

PHATRDRAFT_44547 - ankyrin repeat (Pho88 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44547
PHATRDRAFT_44858 spc25_schpo kinetochore protein spc25 (Spindle_Spc25)

PHATRDRAFT_44858 - spc25_schpo kinetochore protein spc25 (Spindle_Spc25)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44858
PHATRDRAFT_44874

PHATRDRAFT_44874 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44874
PHATRDRAFT_45621 hmp_bacsu flavohemoprotein (hemoglobin-like protein)(nitric oxide dioxygenase) (no oxygenase) (PRK13289)

PHATRDRAFT_45621 - hmp_bacsu flavohemoprotein (hemoglobin-like protein)(nitric oxide dioxygenase) (no oxygenase) (PRK13289)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45621
PHATRDRAFT_45650 nuclear pore protein (RanBD_family)

PHATRDRAFT_45650 - nuclear pore protein (RanBD_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45650
PHATRDRAFT_46021 serine threonine rich antigen

PHATRDRAFT_46021 - serine threonine rich antigen

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46021
PHATRDRAFT_46074 aspartyl asparaginyl beta-hydroxylase (Asp_Arg_Hydrox superfamily)

PHATRDRAFT_46074 - aspartyl asparaginyl beta-hydroxylase (Asp_Arg_Hydrox superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46074
PHATRDRAFT_47054 taf12 rna polymerasetata box binding protein-associated factor (TAF12)

PHATRDRAFT_47054 - taf12 rna polymerasetata box binding protein-associated factor (TAF12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47054
PHATRDRAFT_48517 sam-dependent methyltransferases (Cfa)

PHATRDRAFT_48517 - sam-dependent methyltransferases (Cfa)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48517
PHATRDRAFT_9123 gcn4-complementing protein homolog (ArfGap superfamily)

PHATRDRAFT_9123 - gcn4-complementing protein homolog (ArfGap superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9123
GO ID Go Term p-value q-value Cluster
GO:0008610 lipid biosynthesis 0.0000693 0.159914 Phatr_bicluster_0248
GO:0018193 peptidyl-amino acid modification 0.000229788 0.527133 Phatr_bicluster_0248
GO:0006177 GMP biosynthesis 0.0098558 1 Phatr_bicluster_0248
GO:0006164 purine nucleotide biosynthesis 0.0196193 1 Phatr_bicluster_0248
GO:0015780 nucleotide-sugar transport 0.0196193 1 Phatr_bicluster_0248
GO:0009058 biosynthesis 0.0202116 1 Phatr_bicluster_0248
GO:0006888 ER to Golgi transport 0.0388725 1 Phatr_bicluster_0248
GO:0043087 regulation of GTPase activity 0.0530761 1 Phatr_bicluster_0248
GO:0006352 transcription initiation 0.0577662 1 Phatr_bicluster_0248
GO:0006633 fatty acid biosynthesis 0.0624342 1 Phatr_bicluster_0248
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