Phatr_bicluster_0062 Residual: 0.39
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_0062 0.39 Phaeodactylum tricornutum
Displaying 1 - 25 of 25
PHATRDRAFT_10970 zeaxanthin epoxidase precursor (NAD_binding_8 superfamily)

PHATRDRAFT_10970 - zeaxanthin epoxidase precursor (NAD_binding_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10970
PHATRDRAFT_12614 protein kinase 2 beta chain (PTZ00396)

PHATRDRAFT_12614 - protein kinase 2 beta chain (PTZ00396)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12614
PHATRDRAFT_20143 acyl-synthetase long-chain family member 4 (AFD_class_I superfamily)

PHATRDRAFT_20143 - acyl-synthetase long-chain family member 4 (AFD_class_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20143
PHATRDRAFT_20872 (CFTR_protein)

PHATRDRAFT_20872 - (CFTR_protein)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20872
PHATRDRAFT_27429 cry5 protein (FAD_binding_7)

PHATRDRAFT_27429 - cry5 protein (FAD_binding_7)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27429
PHATRDRAFT_31632

PHATRDRAFT_31632 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31632
PHATRDRAFT_31764 hsf-type dna-binding domain containing protein (HSF_DNA-bind superfamily)

PHATRDRAFT_31764 - hsf-type dna-binding domain containing protein (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31764
PHATRDRAFT_33928

PHATRDRAFT_33928 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33928
PHATRDRAFT_34119 cysteine desulfurylase (AAT_I superfamily)

PHATRDRAFT_34119 - cysteine desulfurylase (AAT_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34119
PHATRDRAFT_3527 at5g47860 mca23_20 (DUF1350 superfamily)

PHATRDRAFT_3527 - at5g47860 mca23_20 (DUF1350 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3527
PHATRDRAFT_38928

PHATRDRAFT_38928 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38928
PHATRDRAFT_41522

PHATRDRAFT_41522 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41522
PHATRDRAFT_42329 (DUF3529)

PHATRDRAFT_42329 - (DUF3529)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42329
PHATRDRAFT_4266 mgc81751 protein (NADB_Rossmann superfamily)

PHATRDRAFT_4266 - mgc81751 protein (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4266
PHATRDRAFT_43422 tetratricopeptide tpr_2 (NrfG)

PHATRDRAFT_43422 - tetratricopeptide tpr_2 (NrfG)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43422
PHATRDRAFT_44153 dienelactone hydrolase (Abhydrolase_5)

PHATRDRAFT_44153 - dienelactone hydrolase (Abhydrolase_5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44153
PHATRDRAFT_44342

PHATRDRAFT_44342 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44342
PHATRDRAFT_45013 ankyrin repeat (DnaQ_like_exo superfamily)

PHATRDRAFT_45013 - ankyrin repeat (DnaQ_like_exo superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45013
PHATRDRAFT_45022 translation initiation factor if-2

PHATRDRAFT_45022 - translation initiation factor if-2

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45022
PHATRDRAFT_45538 cyclic nucleotide-binding domain protein (CAP_ED)

PHATRDRAFT_45538 - cyclic nucleotide-binding domain protein (CAP_ED)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45538
PHATRDRAFT_49991

PHATRDRAFT_49991 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49991
PHATRDRAFT_50051 at1g67700 f12a21_30

PHATRDRAFT_50051 - at1g67700 f12a21_30

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50051
PHATRDRAFT_50445 at1g70730 f5a18_9 (PLN02307)

PHATRDRAFT_50445 - at1g70730 f5a18_9 (PLN02307)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50445
PHATRDRAFT_974 possible sufe protein (SufE superfamily)

PHATRDRAFT_7639 - possible sufe protein (SufE superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7639

PHATRDRAFT_974 - ubiquitin-specific protease (Peptidase_C19 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_974
GO ID Go Term p-value q-value Cluster
GO:0008152 metabolism 0.00597065 1 Phatr_bicluster_0062
GO:0006725 aromatic compound metabolism 0.0530761 1 Phatr_bicluster_0062
GO:0006281 DNA repair 0.0886914 1 Phatr_bicluster_0062
GO:0006511 ubiquitin-dependent protein catabolism 0.115816 1 Phatr_bicluster_0062
GO:0005975 carbohydrate metabolism 0.158622 1 Phatr_bicluster_0062
GO:0006810 transport 0.412691 1 Phatr_bicluster_0062
GO:0006355 regulation of transcription, DNA-dependent 0.45797 1 Phatr_bicluster_0062
GO:0006118 electron transport 0.473356 1 Phatr_bicluster_0062
Log in to post comments