Phatr_bicluster_0077 Residual: 0.23
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_0077 0.23 Phaeodactylum tricornutum
Displaying 1 - 26 of 26
PHATRDRAFT_14191 af375428_1at4g29590 t16l4_100

PHATRDRAFT_14191 - af375428_1at4g29590 t16l4_100

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14191
PHATRDRAFT_14988

PHATRDRAFT_14988 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14988
PHATRDRAFT_17086 phosphoglycerate mutase 1 family (HP_PGM_like)

PHATRDRAFT_17086 - phosphoglycerate mutase 1 family (HP_PGM_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17086
PHATRDRAFT_18489 solute carrier family 25 (mitochondrial carrier citrate transporter)member 1 (Mito_carr)

PHATRDRAFT_18489 - solute carrier family 25 (mitochondrial carrier citrate transporter)member 1 (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18489
PHATRDRAFT_23547 bifunctional aminoacyl-trna prolyl-trna (PRK08661)

PHATRDRAFT_23547 - bifunctional aminoacyl-trna prolyl-trna (PRK08661)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23547
PHATRDRAFT_23557 cation-efflux transporter (CzcD)

PHATRDRAFT_23557 - cation-efflux transporter (CzcD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23557
PHATRDRAFT_29260 probable transketolase (PLN02790)

PHATRDRAFT_29260 - probable transketolase (PLN02790)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29260
PHATRDRAFT_30145 citrate synthase (CS_ACL-C_CCL superfamily)

PHATRDRAFT_30145 - citrate synthase (CS_ACL-C_CCL superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30145
PHATRDRAFT_33099

PHATRDRAFT_33099 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33099
PHATRDRAFT_33257 af466359_1 swp1

PHATRDRAFT_33257 - af466359_1 swp1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33257
PHATRDRAFT_34371

PHATRDRAFT_34371 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34371
PHATRDRAFT_38009 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase component (lipoyl_domain)

PHATRDRAFT_38009 - pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase component (lipoyl_domain)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38009
PHATRDRAFT_40430 dihydrolipoamide s-succinyltransferase (e2 component of 2-oxo-glutarate complex) (PRK05704)

PHATRDRAFT_40430 - dihydrolipoamide s-succinyltransferase (e2 component of 2-oxo-glutarate complex) (PRK05704)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40430
PHATRDRAFT_42398 malate dehydrogenase (PLN00106)

PHATRDRAFT_42398 - malate dehydrogenase (PLN00106)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42398
PHATRDRAFT_43904 phytoene dehydrogenase (crtI_fam)

PHATRDRAFT_43904 - phytoene dehydrogenase (crtI_fam)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43904
PHATRDRAFT_43905 moloney leukemia virushomolog (AAA_12)

PHATRDRAFT_43905 - moloney leukemia virushomolog (AAA_12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43905
PHATRDRAFT_47883 c330023m02rik protein (NatB_MDM20 superfamily)

PHATRDRAFT_47883 - c330023m02rik protein (NatB_MDM20 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47883
PHATRDRAFT_48625 urease accessory protein (UreD)

PHATRDRAFT_48625 - urease accessory protein (UreD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48625
PHATRDRAFT_48661

PHATRDRAFT_48661 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48661
PHATRDRAFT_49241

PHATRDRAFT_49241 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49241
PHATRDRAFT_49658 pyrroline-5-carboxylate reductase (PRK06476)

PHATRDRAFT_49658 - pyrroline-5-carboxylate reductase (PRK06476)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49658
PHATRDRAFT_49726 abc transporter family protein (3a01204)

PHATRDRAFT_49726 - abc transporter family protein (3a01204)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49726
PHATRDRAFT_50440 4snc-tudor domain protein (SNc)

PHATRDRAFT_50440 - 4snc-tudor domain protein (SNc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50440
PHATRDRAFT_50540 iap100 protein

PHATRDRAFT_50540 - iap100 protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50540
PHATRDRAFT_51271 constans interacting protein 3 (FKBP_C)

PHATRDRAFT_51271 - constans interacting protein 3 (FKBP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51271
PHATRDRAFT_54787 udp-glucose:glycoprotein glucosyltransferase (Glyco_tranf_GTA_type superfamily)

PHATRDRAFT_54787 - udp-glucose:glycoprotein glucosyltransferase (Glyco_tranf_GTA_type superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54787
GO ID Go Term p-value q-value Cluster
GO:0006099 tricarboxylic acid cycle 0.000457819 1 Phatr_bicluster_0077
GO:0006092 main pathways of carbohydrate metabolism 0.00419857 1 Phatr_bicluster_0077
GO:0006108 malate metabolism 0.00419857 1 Phatr_bicluster_0077
GO:0006433 prolyl-tRNA aminoacylation 0.00419857 1 Phatr_bicluster_0077
GO:0006100 tricarboxylic acid cycle intermediate metabolism 0.00419857 1 Phatr_bicluster_0077
GO:0016117 carotenoid biosynthesis 0.012546 1 Phatr_bicluster_0077
GO:0006561 proline biosynthesis 0.0208275 1 Phatr_bicluster_0077
GO:0006807 nitrogen compound metabolism 0.057292 1 Phatr_bicluster_0077
GO:0006812 cation transport 0.107713 1 Phatr_bicluster_0077
GO:0006096 glycolysis 0.137467 1 Phatr_bicluster_0077
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