Phatr_bicluster_0022 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_0022 0.39 Phaeodactylum tricornutum
Displaying 1 - 34 of 34
PHATRDRAFT_10585 dna ligase i (Adenylation_DNA_ligase_like superfamily)

PHATRDRAFT_10585 - dna ligase i (Adenylation_DNA_ligase_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10585
PHATRDRAFT_15374 seryl-trna synthetase (PRK05431)

PHATRDRAFT_15374 - seryl-trna synthetase (PRK05431)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15374
PHATRDRAFT_16843 centromere-specific histone h3 (H4 superfamily)

PHATRDRAFT_16843 - centromere-specific histone h3 (H4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16843
PHATRDRAFT_18202 cg8798-isoform b (lon)

PHATRDRAFT_18202 - cg8798-isoform b (lon)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18202
PHATRDRAFT_21789 tcpg_thawet-complex protein 1 subunit gamma (tcp-1-gamma) (cct-gamma) (TCP1_gamma)

PHATRDRAFT_21789 - tcpg_thawet-complex protein 1 subunit gamma (tcp-1-gamma) (cct-gamma) (TCP1_gamma)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21789
PHATRDRAFT_22803 atp-binding protein of abc transporter (ABCD_peroxisomal_ALDP)

PHATRDRAFT_22803 - atp-binding protein of abc transporter (ABCD_peroxisomal_ALDP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22803
PHATRDRAFT_25298 zinc finger protein 259 (Zpr1)

PHATRDRAFT_25298 - zinc finger protein 259 (Zpr1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25298
PHATRDRAFT_26336 uracil phosphoribosyltransferase (PRTases_typeI)

PHATRDRAFT_26336 - uracil phosphoribosyltransferase (PRTases_typeI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26336
PHATRDRAFT_27278 fucoxanthin chlorophyll a c binding protein (Chloroa_b-bind)

PHATRDRAFT_27278 - fucoxanthin chlorophyll a c binding protein (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27278
PHATRDRAFT_29488 delta 6 fatty acid desaturase d6 (PLN03199)

PHATRDRAFT_29488 - delta 6 fatty acid desaturase d6 (PLN03199)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29488
PHATRDRAFT_32850

PHATRDRAFT_32850 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32850
PHATRDRAFT_37743

PHATRDRAFT_37743 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37743
PHATRDRAFT_40470

PHATRDRAFT_40470 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40470
PHATRDRAFT_42686 seed maturation-like protein (DUF760)

PHATRDRAFT_42457 - seed maturation-like protein (DUF760)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42457
PHATRDRAFT_43124

PHATRDRAFT_42686 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42686
PHATRDRAFT_43679 (DUF4168)

PHATRDRAFT_43124 - (DUF4168)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43124
PHATRDRAFT_43964

PHATRDRAFT_43679 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43679
PHATRDRAFT_44170

PHATRDRAFT_43964 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43964
PHATRDRAFT_44756

PHATRDRAFT_44170 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44170
PHATRDRAFT_45605 abcfamily transporter: whiteprotein (3a01204)

PHATRDRAFT_44756 - abcfamily transporter: whiteprotein (3a01204)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44756
PHATRDRAFT_46808 iron ascorbate oxidoreductase family (PTZ00273)

PHATRDRAFT_45605 - iron ascorbate oxidoreductase family (PTZ00273)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45605
PHATRDRAFT_47145 fk506 binding protein 8 (FKBP_C)

PHATRDRAFT_46808 - fk506 binding protein 8 (FKBP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46808
PHATRDRAFT_47968

PHATRDRAFT_47145 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47145
PHATRDRAFT_49054 (Chorein_N)

PHATRDRAFT_47968 - (Chorein_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47968
PHATRDRAFT_49256 proteasome-interacting protein (ANK)

PHATRDRAFT_49054 - proteasome-interacting protein (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49054
PHATRDRAFT_49279

PHATRDRAFT_49256 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49256
PHATRDRAFT_49297 (SMC_prok_B)

PHATRDRAFT_49279 - (SMC_prok_B)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49279
PHATRDRAFT_49306 ribosomal protein s5

PHATRDRAFT_49297 - ribosomal protein s5

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49297
PHATRDRAFT_49659

PHATRDRAFT_49306 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49306
PHATRDRAFT_49666 (Sulfatase superfamily)

PHATRDRAFT_49659 - (Sulfatase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49659
PHATRDRAFT_49670 disease resistance family protein

PHATRDRAFT_49666 - disease resistance family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49666
PHATRDRAFT_50349 disease resistance protein

PHATRDRAFT_49670 - disease resistance protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49670
PHATRDRAFT_54330

PHATRDRAFT_50349 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50349

PHATRDRAFT_54330 - multi-sensor signal transduction histidine kinase (COG4251)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54330
GO ID Go Term p-value q-value Cluster
GO:0006434 seryl-tRNA aminoacylation 0.00887241 1 Phatr_bicluster_0022
GO:0006510 ATP-dependent proteolysis 0.0132807 1 Phatr_bicluster_0022
GO:0017000 antibiotic biosynthesis 0.0220418 1 Phatr_bicluster_0022
GO:0044267 cellular protein metabolism 0.0436241 1 Phatr_bicluster_0022
GO:0006636 fatty acid desaturation 0.0436241 1 Phatr_bicluster_0022
GO:0006334 nucleosome assembly 0.0689292 1 Phatr_bicluster_0022
GO:0007001 chromosome organization and biogenesis (sensu Eukaryota) 0.0730847 1 Phatr_bicluster_0022
GO:0006260 DNA replication 0.109704 1 Phatr_bicluster_0022
GO:0006812 cation transport 0.113688 1 Phatr_bicluster_0022
GO:0006281 DNA repair 0.141104 1 Phatr_bicluster_0022
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