Phatr_bicluster_0217 Residual: 0.19
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_0217 0.19 Phaeodactylum tricornutum
Displaying 1 - 24 of 24
PHATRDRAFT_11006 light-harvesting protein (Chloroa_b-bind)

PHATRDRAFT_11006 - light-harvesting protein (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11006
PHATRDRAFT_14442 light-harvesting protein (Chloroa_b-bind superfamily)

PHATRDRAFT_14442 - light-harvesting protein (Chloroa_b-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14442
PHATRDRAFT_17326 low molecular mass early light-inducible protein hv60

PHATRDRAFT_17326 - low molecular mass early light-inducible protein hv60

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17326
PHATRDRAFT_17531 fucoxanthin chlorophyll a c binding protein (Chloroa_b-bind)

PHATRDRAFT_17531 - fucoxanthin chlorophyll a c binding protein (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17531
PHATRDRAFT_17766 chloroplast light harvesting protein isoform 12 (Chloroa_b-bind superfamily)

PHATRDRAFT_17766 - chloroplast light harvesting protein isoform 12 (Chloroa_b-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17766
PHATRDRAFT_18049 chlorophyll protein 1 (PLN00120)

PHATRDRAFT_18049 - chlorophyll protein 1 (PLN00120)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18049
PHATRDRAFT_20331 oxygen-evolving enhancer protein 1 precursor (MSP superfamily)

PHATRDRAFT_20331 - oxygen-evolving enhancer protein 1 precursor (MSP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20331
PHATRDRAFT_22006 fucoxanthin chlorophyll protein 3 (PLN00120)

PHATRDRAFT_22006 - fucoxanthin chlorophyll protein 3 (PLN00120)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22006
PHATRDRAFT_22680 chloroplast light harvesting protein isoform 15 (Chloroa_b-bind superfamily)

PHATRDRAFT_22680 - chloroplast light harvesting protein isoform 15 (Chloroa_b-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22680
PHATRDRAFT_22956 light-harvesting protein (Chloroa_b-bind)

PHATRDRAFT_22956 - light-harvesting protein (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22956
PHATRDRAFT_23257 chloroplast light harvesting protein isoform 14 (Chloroa_b-bind superfamily)

PHATRDRAFT_23257 - chloroplast light harvesting protein isoform 14 (Chloroa_b-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23257
PHATRDRAFT_25172 fcpb_phatrfucoxanthin-chlorophyll a-c binding proteinchloroplast precursor (PLN00120)

PHATRDRAFT_25172 - fcpb_phatrfucoxanthin-chlorophyll a-c binding proteinchloroplast precursor (PLN00120)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25172
PHATRDRAFT_25893 light-harvesting chlorophyll a-c binding protein (Chloroa_b-bind superfamily)

PHATRDRAFT_25893 - light-harvesting chlorophyll a-c binding protein (Chloroa_b-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25893
PHATRDRAFT_26293 chloroplast photosystem ii 12 kda extrinsic protein (PsbU)

PHATRDRAFT_26293 - chloroplast photosystem ii 12 kda extrinsic protein (PsbU)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26293
PHATRDRAFT_29266 fcpb_phatrfucoxanthin-chlorophyll a-c binding proteinchloroplast precursor (PLN00120)

PHATRDRAFT_29266 - fcpb_phatrfucoxanthin-chlorophyll a-c binding proteinchloroplast precursor (PLN00120)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29266
PHATRDRAFT_30031 light harvesting protein (PLN00120)

PHATRDRAFT_30031 - light harvesting protein (PLN00120)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30031
PHATRDRAFT_30643 fcpb_phatrfucoxanthin-chlorophyll a-c binding proteinchloroplast precursor (PLN00120)

PHATRDRAFT_30643 - fcpb_phatrfucoxanthin-chlorophyll a-c binding proteinchloroplast precursor (PLN00120)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30643
PHATRDRAFT_30648 fucoxanthin chlorophyll protein 3 (PLN00120)

PHATRDRAFT_30648 - fucoxanthin chlorophyll protein 3 (PLN00120)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30648
PHATRDRAFT_43689

PHATRDRAFT_43689 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43689
PHATRDRAFT_46529

PHATRDRAFT_46529 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46529
PHATRDRAFT_51230 fcpf_phatrfucoxanthin-chlorophyll a-c binding proteinchloroplast precursor (PLN00120)

PHATRDRAFT_51230 - fcpf_phatrfucoxanthin-chlorophyll a-c binding proteinchloroplast precursor (PLN00120)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51230
PHATRDRAFT_54027 light-harvesting protein (Chloroa_b-bind superfamily)

PHATRDRAFT_54027 - light-harvesting protein (Chloroa_b-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54027
PHATRDRAFT_54499

PHATRDRAFT_54499 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54499
PHATRDRAFT_6062 light-harvesting protein (Chloroa_b-bind)

PHATRDRAFT_6062 - light-harvesting protein (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6062
GO ID Go Term p-value q-value Cluster
GO:0009765 photosynthesis light harvesting 5.21e-33 1.21e-29 Phatr_bicluster_0217
GO:0042549 photosystem II stabilization 0.0000256 0.0592446 Phatr_bicluster_0217
GO:0015979 photosynthesis 0.0205926 1 Phatr_bicluster_0217
GO:0007186 G-protein coupled receptor protein signaling pathway 0.0654593 1 Phatr_bicluster_0217
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