Phatr_bicluster_0098 Residual: 0.29
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_0098 0.29 Phaeodactylum tricornutum
Displaying 1 - 34 of 34
PHATRDRAFT_10666 aminoacyl-trna synthetase cofactor (tRNA_bind_EMAP-II_like)

PHATRDRAFT_10666 - aminoacyl-trna synthetase cofactor (tRNA_bind_EMAP-II_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10666
PHATRDRAFT_10821 dna-directed rna polymerase (PLN00032)

PHATRDRAFT_10821 - dna-directed rna polymerase (PLN00032)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10821
PHATRDRAFT_10847 30s ribosomal protein s1 (S1_like superfamily)

PHATRDRAFT_10847 - 30s ribosomal protein s1 (S1_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10847
PHATRDRAFT_11088 leucyl-trnacytoplasmic (leucine--trna ligase) (PLN02959)

PHATRDRAFT_11088 - leucyl-trnacytoplasmic (leucine--trna ligase) (PLN02959)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11088
PHATRDRAFT_13382 chloroplast ribose-5-phosphate isomerase (RPI_A)

PHATRDRAFT_13382 - chloroplast ribose-5-phosphate isomerase (RPI_A)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13382
PHATRDRAFT_13682 rssa_soybn40s ribosomal protein sa (PTZ00254)

PHATRDRAFT_13682 - rssa_soybn40s ribosomal protein sa (PTZ00254)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13682
PHATRDRAFT_14366 (PTZ00168)

PHATRDRAFT_14366 - (PTZ00168)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14366
PHATRDRAFT_15032 ribulose-phosphate 3-epimerase (GrpE)

PHATRDRAFT_15032 - ribulose-phosphate 3-epimerase (GrpE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15032
PHATRDRAFT_17059 conserved hypothetical portein

PHATRDRAFT_17059 - conserved hypothetical portein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17059
PHATRDRAFT_17304 methionine aminopeptidase (PTZ00053)

PHATRDRAFT_17304 - methionine aminopeptidase (PTZ00053)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17304
PHATRDRAFT_17772 (PLN03206)

PHATRDRAFT_17772 - (PLN03206)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17772
PHATRDRAFT_1874 eukaryotic translation initiation factorsubunit 6 interacting protein (Paf67 superfamily)

PHATRDRAFT_1874 - eukaryotic translation initiation factorsubunit 6 interacting protein (Paf67 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1874
PHATRDRAFT_21430 t-complex protein 1 subunit epsilon (tcp-1-epsilon) (cct-epsilon) (TCP1_epsilon)

PHATRDRAFT_21430 - t-complex protein 1 subunit epsilon (tcp-1-epsilon) (cct-epsilon) (TCP1_epsilon)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21430
PHATRDRAFT_23871 aspartate aminotransferase mitochondrial precursor (Aminotran_1_2)

PHATRDRAFT_23871 - aspartate aminotransferase mitochondrial precursor (Aminotran_1_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23871
PHATRDRAFT_33885 phenylalanine-trna synthetase-beta subunit (PLN02265)

PHATRDRAFT_27709 - phenylalanine-trna synthetase-beta subunit (PLN02265)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27709
PHATRDRAFT_35810 (Img2 superfamily)

PHATRDRAFT_33885 - (Img2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33885
PHATRDRAFT_39526 mitochondrial import inner membrane translocase subunit (Tim17 superfamily)

PHATRDRAFT_35810 - mitochondrial import inner membrane translocase subunit (Tim17 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35810
PHATRDRAFT_41702 eif3s2 protein (WD40 superfamily)

PHATRDRAFT_39526 - eif3s2 protein (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39526
PHATRDRAFT_41745 tryptophan synthase beta chain (Trp-synth_B)

PHATRDRAFT_41702 - tryptophan synthase beta chain (Trp-synth_B)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41702
PHATRDRAFT_43144 loc496075 protein (UPF0160)

PHATRDRAFT_41745 - loc496075 protein (UPF0160)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41745
PHATRDRAFT_43429 at5g11350 f2i11_240 (EEP superfamily)

PHATRDRAFT_43144 - at5g11350 f2i11_240 (EEP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43144
PHATRDRAFT_43827 chorismate synthase (Chorismate_synthase)

PHATRDRAFT_43429 - chorismate synthase (Chorismate_synthase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43429
PHATRDRAFT_44311

PHATRDRAFT_43827 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43827
PHATRDRAFT_44618 sam-dependent methyltransferase-like (COG1092)

PHATRDRAFT_44311 - sam-dependent methyltransferase-like (COG1092)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44311
PHATRDRAFT_45592 2-isopropylmalate synthase (PLN02321)

PHATRDRAFT_44618 - 2-isopropylmalate synthase (PLN02321)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44618
PHATRDRAFT_51430 spermidine putrescine abc transporter atp-binding subunit (PGDH_like_3)

PHATRDRAFT_45592 - spermidine putrescine abc transporter atp-binding subunit (PGDH_like_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45592
PHATRDRAFT_522 glutamine-trna ligase (PLN03233)

PHATRDRAFT_51430 - glutamine-trna ligase (PLN03233)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51430
PHATRDRAFT_5873 eukaryotic translation initiation factor 3 subunit 8 (eIF-3c_N superfamily)

PHATRDRAFT_522 - eukaryotic translation initiation factor 3 subunit 8 (eIF-3c_N superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_522
PHATRDRAFT_7664 tetratricopeptide repeat domain 35

PHATRDRAFT_5873 - tetratricopeptide repeat domain 35

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5873
PHATRDRAFT_8755 shikimate 5-dehydrogenase (NAD_bind_Shikimate_DH)

PHATRDRAFT_7664 - shikimate 5-dehydrogenase (NAD_bind_Shikimate_DH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7664
PHATRDRAFT_8976 asparaginyl-trna synthetase (asnC)

PHATRDRAFT_8755 - asparaginyl-trna synthetase (asnC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8755
PHATRDRAFT_9199 translation initiation factor 1a (S1_IF1A)

PHATRDRAFT_8976 - translation initiation factor 1a (S1_IF1A)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8976
PHATRDRAFT_9538 cytoplasmic ribosomal protein s13 (PTZ00072)

PHATRDRAFT_9199 - cytoplasmic ribosomal protein s13 (PTZ00072)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9199

PHATRDRAFT_9538 - sulfiteferredoxin dependent (PLN00178)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9538
GO ID Go Term p-value q-value Cluster
GO:0009052 pentose-phosphate shunt, non-oxidative branch 0.00691529 1 Phatr_bicluster_0098
GO:0006413 translational initiation 0.0115874 1 Phatr_bicluster_0098
GO:0006421 asparaginyl-tRNA aminoacylation 0.0137845 1 Phatr_bicluster_0098
GO:0019752 carboxylic acid metabolism 0.0137845 1 Phatr_bicluster_0098
GO:0006432 phenylalanyl-tRNA aminoacylation 0.0206078 1 Phatr_bicluster_0098
GO:0009098 leucine biosynthesis 0.0206078 1 Phatr_bicluster_0098
GO:0006412 protein biosynthesis 0.023407 1 Phatr_bicluster_0098
GO:0009073 aromatic amino acid family biosynthesis 0.0341181 1 Phatr_bicluster_0098
GO:0006189 'de novo' IMP biosynthesis 0.0341181 1 Phatr_bicluster_0098
GO:0006422 aspartyl-tRNA aminoacylation 0.0408058 1 Phatr_bicluster_0098
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