Phatr_bicluster_0088 Residual: 0.33
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_0088 0.33 Phaeodactylum tricornutum
Displaying 1 - 37 of 37
PHATRDRAFT_13233 diguanylate cyclase with gaf sensor

PHATRDRAFT_13233 - diguanylate cyclase with gaf sensor

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13233
PHATRDRAFT_14908 rna polymerase sigma factor (Sig70-cyanoRpoD)

PHATRDRAFT_14908 - rna polymerase sigma factor (Sig70-cyanoRpoD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14908
PHATRDRAFT_16540 aldehyde dehydrogenase 3member b1 (ALDH_F3-13-14_CALDH-like)

PHATRDRAFT_16540 - aldehyde dehydrogenase 3member b1 (ALDH_F3-13-14_CALDH-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16540
PHATRDRAFT_19518 serine racemase (PRK08198)

PHATRDRAFT_19518 - serine racemase (PRK08198)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19518
PHATRDRAFT_22315 mitochondrial carrier protein (Mito_carr)

PHATRDRAFT_22315 - mitochondrial carrier protein (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22315
PHATRDRAFT_31436 peroxisomal membrane protein22kda (Mpv17_PMP22)

PHATRDRAFT_31436 - peroxisomal membrane protein22kda (Mpv17_PMP22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31436
PHATRDRAFT_31925 glutathione s-transferase omegaisoform cra_a (GST_C_family)

PHATRDRAFT_31925 - glutathione s-transferase omegaisoform cra_a (GST_C_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31925
PHATRDRAFT_32875

PHATRDRAFT_32875 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32875
PHATRDRAFT_33920 (MerC)

PHATRDRAFT_33920 - (MerC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33920
PHATRDRAFT_34531

PHATRDRAFT_34531 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34531
PHATRDRAFT_34957 selw selh selenoprotein (Rdx)

PHATRDRAFT_34957 - selw selh selenoprotein (Rdx)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34957
PHATRDRAFT_37532 (SRPBCC superfamily)

PHATRDRAFT_37532 - (SRPBCC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37532
PHATRDRAFT_38534 at3g06050 f24f17_3 (Thioredoxin_like superfamily)

PHATRDRAFT_38534 - at3g06050 f24f17_3 (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38534
PHATRDRAFT_38632

PHATRDRAFT_38632 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38632
PHATRDRAFT_38633

PHATRDRAFT_38633 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38633
PHATRDRAFT_38634 retinol binding proteincellular

PHATRDRAFT_38634 - retinol binding proteincellular

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38634
PHATRDRAFT_40695 cog0596: hydrolases or acyltransferases (alpha beta hydrolase superfamily) (Abhydrolase_6)

PHATRDRAFT_40695 - cog0596: hydrolases or acyltransferases (alpha beta hydrolase superfamily) (Abhydrolase_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40695
PHATRDRAFT_43618

PHATRDRAFT_43618 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43618
PHATRDRAFT_43896 atp-dependent clp protease adaptor protein (ClpS)

PHATRDRAFT_43896 - atp-dependent clp protease adaptor protein (ClpS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43896
PHATRDRAFT_44376

PHATRDRAFT_44376 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44376
PHATRDRAFT_44704 protein n-terminal asparagine amidohydrolase (N_Asn_amidohyd superfamily)

PHATRDRAFT_44704 - protein n-terminal asparagine amidohydrolase (N_Asn_amidohyd superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44704
PHATRDRAFT_44968 ectonucleoside triphosphate diphosphohydrolase 4 (GDA1_CD39 superfamily)

PHATRDRAFT_44968 - ectonucleoside triphosphate diphosphohydrolase 4 (GDA1_CD39 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44968
PHATRDRAFT_45186

PHATRDRAFT_45186 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45186
PHATRDRAFT_45867

PHATRDRAFT_45867 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45867
PHATRDRAFT_46768 epsk domain protein (Branch superfamily)

PHATRDRAFT_46768 - epsk domain protein (Branch superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46768
PHATRDRAFT_47188 nod3isoform cra_d (LRR_RI superfamily)

PHATRDRAFT_47188 - nod3isoform cra_d (LRR_RI superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47188
PHATRDRAFT_47335

PHATRDRAFT_47335 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47335
PHATRDRAFT_47439 f-box only protein 31 (DUF3506 superfamily)

PHATRDRAFT_47439 - f-box only protein 31 (DUF3506 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47439
PHATRDRAFT_48225 nod2 protein (LRR_RI superfamily)

PHATRDRAFT_48225 - nod2 protein (LRR_RI superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48225
PHATRDRAFT_48309

PHATRDRAFT_48309 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48309
PHATRDRAFT_48941

PHATRDRAFT_48941 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48941
PHATRDRAFT_48944

PHATRDRAFT_48944 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48944
PHATRDRAFT_49097 vitelliform macular dystrophy 2-like protein 2 (Bestrophin superfamily)

PHATRDRAFT_49097 - vitelliform macular dystrophy 2-like protein 2 (Bestrophin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49097
PHATRDRAFT_49336 gcn5-related n-acetyltransferase (NAT_SF)

PHATRDRAFT_49336 - gcn5-related n-acetyltransferase (NAT_SF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49336
PHATRDRAFT_50481 heat shock factor rhsf2 (HSF_DNA-bind superfamily)

PHATRDRAFT_50481 - heat shock factor rhsf2 (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50481
PHATRDRAFT_54435

PHATRDRAFT_54435 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54435
PHATRDRAFT_8167 thioredoxin (TRX_family)

PHATRDRAFT_8167 - thioredoxin (TRX_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8167
GO ID Go Term p-value q-value Cluster
GO:0006352 transcription initiation 0.0205774 1 Phatr_bicluster_0088
GO:0006355 regulation of transcription, DNA-dependent 0.0510752 1 Phatr_bicluster_0088
GO:0008152 metabolism 0.0865285 1 Phatr_bicluster_0088
GO:0006810 transport 0.287164 1 Phatr_bicluster_0088
GO:0006118 electron transport 0.33492 1 Phatr_bicluster_0088
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