Phatr_bicluster_0125 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_0125 0.29 Phaeodactylum tricornutum
Displaying 1 - 35 of 35
PHATRDRAFT_11735 26s proteasome aaa-atpase subunit rpt3 (PTZ00454)

PHATRDRAFT_11735 - 26s proteasome aaa-atpase subunit rpt3 (PTZ00454)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11735
PHATRDRAFT_13622 mgc83233 protein (RPN1)

PHATRDRAFT_13622 - mgc83233 protein (RPN1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13622
PHATRDRAFT_19004 proteasome subunit alpha type 7 (proteasome_alpha_type_7)

PHATRDRAFT_19004 - proteasome subunit alpha type 7 (proteasome_alpha_type_7)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19004
PHATRDRAFT_19300 loc446265 protein (RPN2)

PHATRDRAFT_19300 - loc446265 protein (RPN2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19300
PHATRDRAFT_19341 proteasome chain protein (proteasome_beta_type_2)

PHATRDRAFT_19341 - proteasome chain protein (proteasome_beta_type_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19341
PHATRDRAFT_20227 26s proteasome regulatory complex subunit rpn11 (MPN_RPN11_CSN5)

PHATRDRAFT_20227 - 26s proteasome regulatory complex subunit rpn11 (MPN_RPN11_CSN5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20227
PHATRDRAFT_20434 at1g64520 f1n19_10 (SAC3_GANP)

PHATRDRAFT_20434 - at1g64520 f1n19_10 (SAC3_GANP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20434
PHATRDRAFT_24865 proteasome 26s non-atpase subunit 12 (PCI superfamily)

PHATRDRAFT_24865 - proteasome 26s non-atpase subunit 12 (PCI superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24865
PHATRDRAFT_28202 20s proteasome alpha subunit e (proteasome_alpha_type_5)

PHATRDRAFT_28202 - 20s proteasome alpha subunit e (proteasome_alpha_type_5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28202
PHATRDRAFT_28219 26s proteasome atpase subunit (RPT1)

PHATRDRAFT_28219 - 26s proteasome atpase subunit (RPT1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28219
PHATRDRAFT_30003 proteasomebeta type 3 (proteasome_beta_type_3)

PHATRDRAFT_30003 - proteasomebeta type 3 (proteasome_beta_type_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30003
PHATRDRAFT_30067 26s proteasome regulatory particle triple-a atpase subunit6 (RPT1)

PHATRDRAFT_30067 - 26s proteasome regulatory particle triple-a atpase subunit6 (RPT1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30067
PHATRDRAFT_33525 heat shock protein 33 (HSP33)

PHATRDRAFT_33525 - heat shock protein 33 (HSP33)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33525
PHATRDRAFT_41172 calr_chlrecalreticulin precursor (Calreticulin)

PHATRDRAFT_41172 - calr_chlrecalreticulin precursor (Calreticulin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41172
PHATRDRAFT_41778 26s proteasome subunit 4 (AAA)

PHATRDRAFT_41778 - 26s proteasome subunit 4 (AAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41778
PHATRDRAFT_42566 protein disulfide-isomerase-like proteinep2 precursor (PDI_a_family)

PHATRDRAFT_42566 - protein disulfide-isomerase-like proteinep2 precursor (PDI_a_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42566
PHATRDRAFT_42757 p23 co-chaperone of hsp90 system (p23_hB-ind1_like)

PHATRDRAFT_42757 - p23 co-chaperone of hsp90 system (p23_hB-ind1_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42757
PHATRDRAFT_45122 26s proteasome regulatory complex atpase rpt4 (RPT1)

PHATRDRAFT_45122 - 26s proteasome regulatory complex atpase rpt4 (RPT1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45122
PHATRDRAFT_47062 armadillo beta-catenin repeat family protein

PHATRDRAFT_47062 - armadillo beta-catenin repeat family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47062
PHATRDRAFT_47306 protein disulfide isomerase (PDI_a_family)

PHATRDRAFT_47306 - protein disulfide isomerase (PDI_a_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47306
PHATRDRAFT_47887 proteasome activator subunit 1 (PA28_beta superfamily)

PHATRDRAFT_47887 - proteasome activator subunit 1 (PA28_beta superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47887
PHATRDRAFT_47905 nucleic acid binding protein (CSP_CDS)

PHATRDRAFT_47905 - nucleic acid binding protein (CSP_CDS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47905
PHATRDRAFT_47918 regulatory protein suaprga1 (MAM33 superfamily)

PHATRDRAFT_47918 - regulatory protein suaprga1 (MAM33 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47918
PHATRDRAFT_49086

PHATRDRAFT_49086 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49086
PHATRDRAFT_49172 (zf-Tim10_DDP)

PHATRDRAFT_49172 - (zf-Tim10_DDP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49172
PHATRDRAFT_49301

PHATRDRAFT_49301 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49301
PHATRDRAFT_49897 20s proteasome alpha subunit (proteasome_alpha_type_2)

PHATRDRAFT_49897 - 20s proteasome alpha subunit (proteasome_alpha_type_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49897
PHATRDRAFT_51280 signal peptidase i (S26_SPase_I)

PHATRDRAFT_51280 - signal peptidase i (S26_SPase_I)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51280
PHATRDRAFT_51691 beta 1 subunit of 20s proteasome (proteasome_beta_type_6)

PHATRDRAFT_51691 - beta 1 subunit of 20s proteasome (proteasome_beta_type_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51691
PHATRDRAFT_52198 (RPN6)

PHATRDRAFT_52198 - (RPN6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52198
PHATRDRAFT_5311 proteasome subunit beta 7 (proteasome_beta_type_7)

PHATRDRAFT_5311 - proteasome subunit beta 7 (proteasome_beta_type_7)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5311
PHATRDRAFT_54971 (Smc)

PHATRDRAFT_54971 - (Smc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54971
PHATRDRAFT_55079 pyruvate kinase (PRK05826)

PHATRDRAFT_55079 - pyruvate kinase (PRK05826)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55079
PHATRDRAFT_55215 heat shock (PRK05218)

PHATRDRAFT_55215 - heat shock (PRK05218)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55215
PHATRDRAFT_5685 pag1 (20s proteasome alpha subunit g1) peptidase (Ntn_hydrolase superfamily)

PHATRDRAFT_5685 - pag1 (20s proteasome alpha subunit g1) peptidase (Ntn_hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5685
GO ID Go Term p-value q-value Cluster
GO:0030163 protein catabolism 0.00000000488 0.0000113 Phatr_bicluster_0125
GO:0006511 ubiquitin-dependent protein catabolism 0.0000000128 0.0000297 Phatr_bicluster_0125
GO:0045039 mitochondrial inner membrane protein import 0.0206078 1 Phatr_bicluster_0125
GO:0006626 protein-mitochondrial targeting 0.0206078 1 Phatr_bicluster_0125
GO:0000074 regulation of cell cycle 0.0225725 1 Phatr_bicluster_0125
GO:0006465 signal peptide processing 0.0273856 1 Phatr_bicluster_0125
GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism 0.0735796 1 Phatr_bicluster_0125
GO:0006260 DNA replication 0.165551 1 Phatr_bicluster_0125
GO:0006457 protein folding 0.193151 1 Phatr_bicluster_0125
GO:0006281 DNA repair 0.210935 1 Phatr_bicluster_0125
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