Phatr_bicluster_0119 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_0119 0.39 Phaeodactylum tricornutum
Displaying 1 - 32 of 32
PHATRDRAFT_12368 myb domain-containing protein (HELICc)

PHATRDRAFT_12368 - myb domain-containing protein (HELICc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12368
PHATRDRAFT_13890 glutamyl-trnaa subunit (Amidase superfamily)

PHATRDRAFT_13890 - glutamyl-trnaa subunit (Amidase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13890
PHATRDRAFT_15323 alpha beta fold family (Abhydrolase_6)

PHATRDRAFT_15323 - alpha beta fold family (Abhydrolase_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15323
PHATRDRAFT_21201 udp-sulfoquinovose synthase (PLN02572)

PHATRDRAFT_21201 - udp-sulfoquinovose synthase (PLN02572)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21201
PHATRDRAFT_25183 carbamoyl-phosphate synthetaseaspartateand dihydroorotase (PLN02527)

PHATRDRAFT_25183 - carbamoyl-phosphate synthetaseaspartateand dihydroorotase (PLN02527)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25183
PHATRDRAFT_28585 af193846_1branched-chain amino acid aminotransferase (PLPDE_IV superfamily)

PHATRDRAFT_28585 - af193846_1branched-chain amino acid aminotransferase (PLPDE_IV superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28585
PHATRDRAFT_30446 chaperonin containingsubunit 4 (TCP1_delta)

PHATRDRAFT_30446 - chaperonin containingsubunit 4 (TCP1_delta)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30446
PHATRDRAFT_32847 glycine cleavage system h protein (GCS_H)

PHATRDRAFT_32847 - glycine cleavage system h protein (GCS_H)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32847
PHATRDRAFT_38736 (DUF1499 superfamily)

PHATRDRAFT_38736 - (DUF1499 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38736
PHATRDRAFT_38794 (Glyco_hydrolase_16 superfamily)

PHATRDRAFT_38794 - (Glyco_hydrolase_16 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38794
PHATRDRAFT_39209 (SET)

PHATRDRAFT_39209 - (SET)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39209
PHATRDRAFT_40349 sec63 cg8583-pa (DnaJ)

PHATRDRAFT_40349 - sec63 cg8583-pa (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40349
PHATRDRAFT_40650 nicotinatenucleotide adenylyltransferase (NMNAT)

PHATRDRAFT_40650 - nicotinatenucleotide adenylyltransferase (NMNAT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40650
PHATRDRAFT_41016 aspartyl-trna synthetase (aspC)

PHATRDRAFT_41016 - aspartyl-trna synthetase (aspC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41016
PHATRDRAFT_42866 oxa12_schpo inner membrane protein oxa1-mitochondrial precursor (cytochrome oxidase biogenesis protein 1-2) (60KD_IMP)

PHATRDRAFT_42866 - oxa12_schpo inner membrane protein oxa1-mitochondrial precursor (cytochrome oxidase biogenesis protein 1-2) (60KD_IMP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42866
PHATRDRAFT_43499 tumor suppressor candidate 4 (NPR2 superfamily)

PHATRDRAFT_43499 - tumor suppressor candidate 4 (NPR2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43499
PHATRDRAFT_43855

PHATRDRAFT_43855 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43855
PHATRDRAFT_44180

PHATRDRAFT_44180 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44180
PHATRDRAFT_44623 (YL1_C)

PHATRDRAFT_44623 - (YL1_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44623
PHATRDRAFT_45680

PHATRDRAFT_45680 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45680
PHATRDRAFT_47545

PHATRDRAFT_47545 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47545
PHATRDRAFT_47829 rieske (2fe-2s) region (Rieske superfamily)

PHATRDRAFT_47829 - rieske (2fe-2s) region (Rieske superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47829
PHATRDRAFT_48391 jmj4_schpo jumonji domain-containing protein 4 (meiotically up-regulated gene 149 protein) (Cupin_8)

PHATRDRAFT_48391 - jmj4_schpo jumonji domain-containing protein 4 (meiotically up-regulated gene 149 protein) (Cupin_8)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48391
PHATRDRAFT_48637 amino acid transporter (Aa_trans superfamily)

PHATRDRAFT_48637 - amino acid transporter (Aa_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48637
PHATRDRAFT_48868

PHATRDRAFT_48868 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48868
PHATRDRAFT_49487 mgc80283 protein (FtsJ)

PHATRDRAFT_49487 - mgc80283 protein (FtsJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49487
PHATRDRAFT_49522 cog3195: uncharacterized protein conserved in bacteria (OHCU_decarbox superfamily)

PHATRDRAFT_49522 - cog3195: uncharacterized protein conserved in bacteria (OHCU_decarbox superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49522
PHATRDRAFT_49610 (BglC)

PHATRDRAFT_49610 - (BglC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49610
PHATRDRAFT_50177 (Glyco_hydrolase_16 superfamily)

PHATRDRAFT_50177 - (Glyco_hydrolase_16 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50177
PHATRDRAFT_50496 hypothetical sam-dependent methyltransferase

PHATRDRAFT_50496 - hypothetical sam-dependent methyltransferase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50496
PHATRDRAFT_51407 polgamma1 (polymerase gamma 1) dna binding dna-directed dna polymerase (DNA_pol_A_plastid_like)

PHATRDRAFT_51407 - polgamma1 (polymerase gamma 1) dna binding dna-directed dna polymerase (DNA_pol_A_plastid_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51407
PHATRDRAFT_7763 flag-tagged protein kinase domain ofmitogen-activated protein kinase kinase kinase (PKc_like superfamily)

PHATRDRAFT_7763 - flag-tagged protein kinase domain ofmitogen-activated protein kinase kinase kinase (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7763
GO ID Go Term p-value q-value Cluster
GO:0006207 'de novo' pyrimidine base biosynthesis 0.0176704 1 Phatr_bicluster_0119
GO:0006422 aspartyl-tRNA aminoacylation 0.0263947 1 Phatr_bicluster_0119
GO:0044267 cellular protein metabolism 0.0436241 1 Phatr_bicluster_0119
GO:0006725 aromatic compound metabolism 0.0854465 1 Phatr_bicluster_0119
GO:0006520 amino acid metabolism 0.101687 1 Phatr_bicluster_0119
GO:0006865 amino acid transport 0.117654 1 Phatr_bicluster_0119
GO:0008152 metabolism 0.137805 1 Phatr_bicluster_0119
GO:0009058 biosynthesis 0.182574 1 Phatr_bicluster_0119
GO:0006810 transport 0.207366 1 Phatr_bicluster_0119
GO:0006418 tRNA aminoacylation for protein translation 0.207972 1 Phatr_bicluster_0119
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