Phatr_bicluster_0102 Residual: 0.21
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_0102 0.21 Phaeodactylum tricornutum
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Displaying 1 - 18 of 18
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PHATRDRAFT_11703 transducin-like 3 (WD40)

PHATRDRAFT_11703 - transducin-like 3 (WD40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11703
PHATRDRAFT_17487 gamma hydroxybutyrate dehydrogenase-like protein (MmsB)

PHATRDRAFT_17487 - gamma hydroxybutyrate dehydrogenase-like protein (MmsB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17487
PHATRDRAFT_2182 matrix attachment region binding protein (SIK1)

PHATRDRAFT_19552 - matrix attachment region binding protein (SIK1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19552
PHATRDRAFT_23582 gtp-binding family protein (Nucleostemin_like)

PHATRDRAFT_2182 - gtp-binding family protein (Nucleostemin_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2182
PHATRDRAFT_30365 importin beta-2 subunit family protein

PHATRDRAFT_23582 - importin beta-2 subunit family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23582
PHATRDRAFT_31494 nog1_arath probable nucleolar gtp-binding protein 1 gb (COG1084)

PHATRDRAFT_30365 - nog1_arath probable nucleolar gtp-binding protein 1 gb (COG1084)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30365
PHATRDRAFT_31718 (PRTases_typeI)

PHATRDRAFT_31494 - (PRTases_typeI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31494
PHATRDRAFT_35020 inosine monophosphate dehydrogenase 1 (PLN02274)

PHATRDRAFT_31718 - inosine monophosphate dehydrogenase 1 (PLN02274)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31718
PHATRDRAFT_44942 (GCIP superfamily)

PHATRDRAFT_35020 - (GCIP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35020
PHATRDRAFT_44970 elongation factor 3

PHATRDRAFT_44942 - elongation factor 3

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44942
PHATRDRAFT_45715 hypothetical conserved protein (THUMP_AdoMetMT)

PHATRDRAFT_44970 - hypothetical conserved protein (THUMP_AdoMetMT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44970
PHATRDRAFT_46516 (SAP)

PHATRDRAFT_45715 - (SAP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45715
PHATRDRAFT_47181 n-acetyltransferase 10 (COG1444)

PHATRDRAFT_46516 - n-acetyltransferase 10 (COG1444)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46516
PHATRDRAFT_48920 heat shock transcription factor 4 isoform 2 (HSF_DNA-bind)

PHATRDRAFT_47181 - heat shock transcription factor 4 isoform 2 (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47181
PHATRDRAFT_54710 loc398434 protein (PTZ00146)

PHATRDRAFT_48920 - loc398434 protein (PTZ00146)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48920
PHATRDRAFT_9372 protein arginine n-methyltransferase prote (AdoMet_MTases)

PHATRDRAFT_54710 - protein arginine n-methyltransferase prote (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54710

PHATRDRAFT_9372 - elongation factor ef-3 (Uup)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9372

PHATRDRAFT_9983 - at5g20160 f5o24_50 (Ribosomal_L7Ae)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9983
GO ID Go Term p-value q-value Cluster
GO:0006573 valine metabolism 0.00591714 1 Phatr_bicluster_0102
GO:0006098 pentose-phosphate shunt 0.0118036 1 Phatr_bicluster_0102
GO:0042254 ribosome biogenesis and assembly 0.0118036 1 Phatr_bicluster_0102
GO:0006364 rRNA processing 0.015711 1 Phatr_bicluster_0102
GO:0006412 protein biosynthesis 0.277391 1 Phatr_bicluster_0102
GO:0006810 transport 0.320848 1 Phatr_bicluster_0102
GO:0006355 regulation of transcription, DNA-dependent 0.359328 1 Phatr_bicluster_0102
GO:0006177 GMP biosynthesis 0.00394818 1 Phatr_bicluster_0102
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