Phatr_bicluster_0053 Residual: 0.47
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_0053 0.47 Phaeodactylum tricornutum
Displaying 1 - 43 of 43
PHATRDRAFT_10299 temporarily assigned gene name family member (tag-321) (DUF2453)

PHATRDRAFT_10299 - temporarily assigned gene name family member (tag-321) (DUF2453)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10299
PHATRDRAFT_10848 cyclic nucleotide-binding domain containing protein (CAP_ED)

PHATRDRAFT_10848 - cyclic nucleotide-binding domain containing protein (CAP_ED)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10848
PHATRDRAFT_10882 -dihydroxy-2-butanone 4-phosphate synthase gtp cyclohydrolase ii (GTP_cyclohydro2)

PHATRDRAFT_10882 - -dihydroxy-2-butanone 4-phosphate synthase gtp cyclohydrolase ii (GTP_cyclohydro2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10882
PHATRDRAFT_14427

PHATRDRAFT_14427 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14427
PHATRDRAFT_17909 peptidyl-prolyl cis-trans isomerase cyclophilin-type family protein (cyclophilin superfamily)

PHATRDRAFT_17909 - peptidyl-prolyl cis-trans isomerase cyclophilin-type family protein (cyclophilin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17909
PHATRDRAFT_19762 (PLN02974)

PHATRDRAFT_19762 - (PLN02974)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19762
PHATRDRAFT_21296 biotin synthase (PLN02389)

PHATRDRAFT_21296 - biotin synthase (PLN02389)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21296
PHATRDRAFT_32219

PHATRDRAFT_32219 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32219
PHATRDRAFT_34694

PHATRDRAFT_34694 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34694
PHATRDRAFT_35637 33 kda ribonucleoprotein (COG0724)

PHATRDRAFT_35561 - 33 kda ribonucleoprotein (COG0724)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35561
PHATRDRAFT_36649 short-chain dehydrogenase reductase sdr (NADB_Rossmann superfamily)

PHATRDRAFT_35637 - short-chain dehydrogenase reductase sdr (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35637
PHATRDRAFT_41189

PHATRDRAFT_36649 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36649
PHATRDRAFT_42876 cyclin d3 (CYCLIN)

PHATRDRAFT_41189 - cyclin d3 (CYCLIN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41189
PHATRDRAFT_42881 abc transporter (PRK11819)

PHATRDRAFT_41857 - abc transporter (PRK11819)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41857
PHATRDRAFT_42981

PHATRDRAFT_42507 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42507
PHATRDRAFT_43311 (Bestrophin superfamily)

PHATRDRAFT_42876 - (Bestrophin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42876
PHATRDRAFT_44263 (ABC_ATPase)

PHATRDRAFT_42881 - (ABC_ATPase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42881
PHATRDRAFT_44641 tetratricopeptide repeat domain containing protein (Aha1_N superfamily)

PHATRDRAFT_42981 - tetratricopeptide repeat domain containing protein (Aha1_N superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42981
PHATRDRAFT_44695 set domain containing protein (SET)

PHATRDRAFT_43311 - set domain containing protein (SET)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43311
PHATRDRAFT_44733

PHATRDRAFT_44263 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44263
PHATRDRAFT_45260 multi-sensor hybrid histidine kinase (bHLH-MYC_N superfamily)

PHATRDRAFT_44641 - multi-sensor hybrid histidine kinase (bHLH-MYC_N superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44641
PHATRDRAFT_45451 m6 (immune inhibitor a) family (M6dom_TIGR03296)

PHATRDRAFT_44695 - m6 (immune inhibitor a) family (M6dom_TIGR03296)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44695
PHATRDRAFT_45498 fucoxanthin chlorophyll a c binding protein (Chloroa_b-bind)

PHATRDRAFT_44733 - fucoxanthin chlorophyll a c binding protein (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44733
PHATRDRAFT_46677 (Aa_trans superfamily)

PHATRDRAFT_45260 - (Aa_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45260
PHATRDRAFT_47022 aliphatic amidase (aliphatic_amidase)

PHATRDRAFT_45451 - aliphatic amidase (aliphatic_amidase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45451
PHATRDRAFT_47158 y1145_vibpa upf0225 protein vp1145 (COG3012)

PHATRDRAFT_45498 - y1145_vibpa upf0225 protein vp1145 (COG3012)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45498
PHATRDRAFT_48068

PHATRDRAFT_46677 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46677
PHATRDRAFT_48545

PHATRDRAFT_47022 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47022
PHATRDRAFT_48579 ae-ubiquitinating function of ataxin-3: insights from the solution structure of the josephin domain (Josephin superfamily)

PHATRDRAFT_47158 - ae-ubiquitinating function of ataxin-3: insights from the solution structure of the josephin domain (Josephin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47158
PHATRDRAFT_48813

PHATRDRAFT_48068 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48068
PHATRDRAFT_49065

PHATRDRAFT_48545 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48545
PHATRDRAFT_49299 alpha 3 frustulin

PHATRDRAFT_48579 - alpha 3 frustulin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48579
PHATRDRAFT_49802

PHATRDRAFT_48813 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48813
PHATRDRAFT_49816 (ACE1-Sec16-like)

PHATRDRAFT_49065 - (ACE1-Sec16-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49065
PHATRDRAFT_50043

PHATRDRAFT_49299 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49299
PHATRDRAFT_50136 (Rhamno_transf superfamily)

PHATRDRAFT_49802 - (Rhamno_transf superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49802
PHATRDRAFT_54101

PHATRDRAFT_49816 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49816
PHATRDRAFT_54493

PHATRDRAFT_50043 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50043
PHATRDRAFT_8741 heat shock factor (HSF_DNA-bind superfamily)

PHATRDRAFT_50136 - heat shock factor (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50136
PHATRDRAFT_9885 nitrate transporter (2A0108)

PHATRDRAFT_54101 - nitrate transporter (2A0108)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54101

PHATRDRAFT_54493 - usp1_soybnudp-sugar pyrophosphorylase 1 (PLN02830)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54493

PHATRDRAFT_8741 - (VHS_ENTH_ANTH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8741

PHATRDRAFT_9885 - mitochondrial carrier protein (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9885
GO ID Go Term p-value q-value Cluster
GO:0009231 riboflavin biosynthesis 0.02058 1 Phatr_bicluster_0053
GO:0006807 nitrogen compound metabolism 0.0474084 1 Phatr_bicluster_0053
GO:0006865 amino acid transport 0.0927227 1 Phatr_bicluster_0053
GO:0000074 regulation of cell cycle 0.111523 1 Phatr_bicluster_0053
GO:0009765 photosynthesis light harvesting 0.126914 1 Phatr_bicluster_0053
GO:0008152 metabolism 0.270353 1 Phatr_bicluster_0053
GO:0006457 protein folding 0.337129 1 Phatr_bicluster_0053
GO:0006468 protein amino acid phosphorylation 0.455951 1 Phatr_bicluster_0053
GO:0006810 transport 0.492171 1 Phatr_bicluster_0053
GO:0006355 regulation of transcription, DNA-dependent 0.541484 1 Phatr_bicluster_0053
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