Phatr_bicluster_0048 Residual: 0.40
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_0048 0.40 Phaeodactylum tricornutum
Displaying 1 - 35 of 35
PHATRDRAFT_10437 (UPF0066)

PHATRDRAFT_10437 - (UPF0066)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10437
PHATRDRAFT_11634 gtpase family protein protein (YihA_EngB)

PHATRDRAFT_11634 - gtpase family protein protein (YihA_EngB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11634
PHATRDRAFT_13606 isn1_yarli imp-specific 5-nucleotidase 1 (ISN1 superfamily)

PHATRDRAFT_13606 - isn1_yarli imp-specific 5-nucleotidase 1 (ISN1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13606
PHATRDRAFT_22027 tim9_mescrmitochondrial import inner membrane translocase subunit tim9 (zf-Tim10_DDP)

PHATRDRAFT_22027 - tim9_mescrmitochondrial import inner membrane translocase subunit tim9 (zf-Tim10_DDP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22027
PHATRDRAFT_228 calcium atpase serca-like (ATPase-IIA1_Ca)

PHATRDRAFT_228 - calcium atpase serca-like (ATPase-IIA1_Ca)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_228
PHATRDRAFT_23375 dihydrouridine synthase (DUS_like_FMN)

PHATRDRAFT_23375 - dihydrouridine synthase (DUS_like_FMN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23375
PHATRDRAFT_31973 protein phosphatase 2c beta (PP2Cc)

PHATRDRAFT_31973 - protein phosphatase 2c beta (PP2Cc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31973
PHATRDRAFT_33369 antifreeze glycoprotein

PHATRDRAFT_33369 - antifreeze glycoprotein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33369
PHATRDRAFT_37523 (PHD)

PHATRDRAFT_37523 - (PHD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37523
PHATRDRAFT_3755 peroxisomal integral membrane protein (Mito_carr)

PHATRDRAFT_3755 - peroxisomal integral membrane protein (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3755
PHATRDRAFT_38095 cl-voltage gated (Voltage_gated_ClC)

PHATRDRAFT_38095 - cl-voltage gated (Voltage_gated_ClC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38095
PHATRDRAFT_39421 chloride channel (Voltage_gated_ClC)

PHATRDRAFT_39421 - chloride channel (Voltage_gated_ClC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39421
PHATRDRAFT_41173

PHATRDRAFT_41173 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41173
PHATRDRAFT_43073

PHATRDRAFT_43073 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43073
PHATRDRAFT_43509

PHATRDRAFT_43509 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43509
PHATRDRAFT_43751

PHATRDRAFT_43751 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43751
PHATRDRAFT_43869 cell surface flocculin

PHATRDRAFT_43869 - cell surface flocculin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43869
PHATRDRAFT_44159 ribosomal protein l11 methyltransferase (prmA)

PHATRDRAFT_44159 - ribosomal protein l11 methyltransferase (prmA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44159
PHATRDRAFT_47431 ser thr protein phosphatase familyexpressed (acc_ester superfamily)

PHATRDRAFT_47431 - ser thr protein phosphatase familyexpressed (acc_ester superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47431
PHATRDRAFT_47578 (Methyltransf_16 superfamily)

PHATRDRAFT_47578 - (Methyltransf_16 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47578
PHATRDRAFT_47614 kiaa0659 protein isoform 3 (Lipase_3)

PHATRDRAFT_47614 - kiaa0659 protein isoform 3 (Lipase_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47614
PHATRDRAFT_47677

PHATRDRAFT_47677 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47677
PHATRDRAFT_47685 bifunctional protein (FolC)

PHATRDRAFT_47685 - bifunctional protein (FolC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47685
PHATRDRAFT_47788 ankyrin repeat (ANK)

PHATRDRAFT_47788 - ankyrin repeat (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47788
PHATRDRAFT_48181

PHATRDRAFT_48181 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48181
PHATRDRAFT_48302 bifunctional phosphopantetheine adenylyl transferase dephosphokinase-like protein (nt_trans superfamily)

PHATRDRAFT_48302 - bifunctional phosphopantetheine adenylyl transferase dephosphokinase-like protein (nt_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48302
PHATRDRAFT_48763 cyclin h-1 (ccl1)

PHATRDRAFT_48763 - cyclin h-1 (ccl1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48763
PHATRDRAFT_49093 (Voltage_gated_ClC)

PHATRDRAFT_49093 - (Voltage_gated_ClC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49093
PHATRDRAFT_49282 viral a-type inclusion

PHATRDRAFT_49282 - viral a-type inclusion

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49282
PHATRDRAFT_49308

PHATRDRAFT_49308 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49308
PHATRDRAFT_49405 peroxisomal biogenesis factor 12 (Pex2_Pex12 superfamily)

PHATRDRAFT_49405 - peroxisomal biogenesis factor 12 (Pex2_Pex12 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49405
PHATRDRAFT_49860 phagocytosis and cell motility protein elmo1-related (ELMO_CED12 superfamily)

PHATRDRAFT_49860 - phagocytosis and cell motility protein elmo1-related (ELMO_CED12 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49860
PHATRDRAFT_50005 gpi-anchored cell surface glycoproteinrequired for diploid pseudohyphal formation and haploid invasivetranscriptionally regulated by the mapk pathway (via ste12p and tec1p) and the camp pathway (via flo8p)

PHATRDRAFT_50005 - gpi-anchored cell surface glycoproteinrequired for diploid pseudohyphal formation and haploid invasivetranscriptionally regulated by the mapk pathway (via ste12p and tec1p) and the camp pathway (via flo8p)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50005
PHATRDRAFT_50075 (SUL1)

PHATRDRAFT_50075 - (SUL1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50075
PHATRDRAFT_50200

PHATRDRAFT_50200 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50200
GO ID Go Term p-value q-value Cluster
GO:0006821 chloride transport 0.00000255 0.00592194 Phatr_bicluster_0048
GO:0009399 nitrogen fixation 0.00887241 1 Phatr_bicluster_0048
GO:0006816 calcium ion transport 0.0132807 1 Phatr_bicluster_0048
GO:0045039 mitochondrial inner membrane protein import 0.0132807 1 Phatr_bicluster_0048
GO:0006626 protein-mitochondrial targeting 0.0132807 1 Phatr_bicluster_0048
GO:0009396 folic acid and derivative biosynthesis 0.0350457 1 Phatr_bicluster_0048
GO:0051341 regulation of oxidoreductase activity 0.0689292 1 Phatr_bicluster_0048
GO:0006629 lipid metabolism 0.0772227 1 Phatr_bicluster_0048
GO:0008033 tRNA processing 0.0854465 1 Phatr_bicluster_0048
GO:0006812 cation transport 0.113688 1 Phatr_bicluster_0048
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