Phatr_bicluster_0024 Residual: 0.42
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_0024 0.42 Phaeodactylum tricornutum
Displaying 1 - 37 of 37
PHATRDRAFT_10567 short chain dehydrogenase (NADB_Rossmann superfamily)

PHATRDRAFT_10567 - short chain dehydrogenase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10567
PHATRDRAFT_12586 ribosomal large subunit pseudouridine synthase d (RluA)

PHATRDRAFT_12586 - ribosomal large subunit pseudouridine synthase d (RluA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12586
PHATRDRAFT_14374 mbf1_canal multiprotein-bridging factor 1 (HTH_XRE)

PHATRDRAFT_14374 - mbf1_canal multiprotein-bridging factor 1 (HTH_XRE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14374
PHATRDRAFT_15294 trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (tRNA_Me_trans)

PHATRDRAFT_15294 - trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (tRNA_Me_trans)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15294
PHATRDRAFT_15777 ferredoxin-nadp oxidoreductase (PLN03116)

PHATRDRAFT_15777 - ferredoxin-nadp oxidoreductase (PLN03116)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15777
PHATRDRAFT_18793 tnf receptor-associated protein (PRK05218)

PHATRDRAFT_18793 - tnf receptor-associated protein (PRK05218)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18793
PHATRDRAFT_21744 calmodulin (PTZ00184)

PHATRDRAFT_21744 - calmodulin (PTZ00184)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21744
PHATRDRAFT_22873 atp adp translocator (PTZ00169)

PHATRDRAFT_22873 - atp adp translocator (PTZ00169)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22873
PHATRDRAFT_30770 af503284_1microsomal cytochrome b5 (Cyt-b5)

PHATRDRAFT_30770 - af503284_1microsomal cytochrome b5 (Cyt-b5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30770
PHATRDRAFT_33159 26s proteasome regulatory chain 4 (PTZ00361)

PHATRDRAFT_33159 - 26s proteasome regulatory chain 4 (PTZ00361)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33159
PHATRDRAFT_37556 transcription factorcyclin-related

PHATRDRAFT_37556 - transcription factorcyclin-related

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37556
PHATRDRAFT_38526 gliotoxin biosynthesis protein

PHATRDRAFT_38526 - gliotoxin biosynthesis protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38526
PHATRDRAFT_39528 (CPSaseII_lrg)

PHATRDRAFT_39528 - (CPSaseII_lrg)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39528
PHATRDRAFT_39710 sam-dependent methyltransferase (Methyltransf_31)

PHATRDRAFT_39710 - sam-dependent methyltransferase (Methyltransf_31)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39710
PHATRDRAFT_41031 sec61 signal peptide plus 9 transmembrane domain-containing protein (PTZ00219)

PHATRDRAFT_41031 - sec61 signal peptide plus 9 transmembrane domain-containing protein (PTZ00219)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41031
PHATRDRAFT_41194

PHATRDRAFT_41194 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41194
PHATRDRAFT_41417 heat shock protein (NBD_sugar-kinase_HSP70_actin superfamily)

PHATRDRAFT_41417 - heat shock protein (NBD_sugar-kinase_HSP70_actin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41417
PHATRDRAFT_42830 3hc4 type family protein (RING)

PHATRDRAFT_42830 - 3hc4 type family protein (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42830
PHATRDRAFT_42867 (LAM superfamily)

PHATRDRAFT_42867 - (LAM superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42867
PHATRDRAFT_43251 adp-ribosylation factor (Arf1_5_like)

PHATRDRAFT_43251 - adp-ribosylation factor (Arf1_5_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43251
PHATRDRAFT_43743

PHATRDRAFT_43743 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43743
PHATRDRAFT_44132 aspartyl asparaginyl beta-hydroxylase (Asp_Arg_Hydrox superfamily)

PHATRDRAFT_44132 - aspartyl asparaginyl beta-hydroxylase (Asp_Arg_Hydrox superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44132
PHATRDRAFT_45227

PHATRDRAFT_45227 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45227
PHATRDRAFT_47402 sym1_neucr protein sym-1 (Mpv17_PMP22)

PHATRDRAFT_47402 - sym1_neucr protein sym-1 (Mpv17_PMP22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47402
PHATRDRAFT_47831 egf-like repeats and discoidin i-like domains 3

PHATRDRAFT_47831 - egf-like repeats and discoidin i-like domains 3

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47831
PHATRDRAFT_48094 proteophosphoglycan ppg4

PHATRDRAFT_48094 - proteophosphoglycan ppg4

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48094
PHATRDRAFT_49892 (DUF1997 superfamily)

PHATRDRAFT_49892 - (DUF1997 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49892
PHATRDRAFT_50006 phytochelatin synthase (Phytochelatin superfamily)

PHATRDRAFT_50006 - phytochelatin synthase (Phytochelatin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50006
PHATRDRAFT_50340

PHATRDRAFT_50340 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50340
PHATRDRAFT_50914 xenobiotic reductase b (OYE_like_FMN)

PHATRDRAFT_50914 - xenobiotic reductase b (OYE_like_FMN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50914
PHATRDRAFT_51604 swi2 snf2-like protein (SNF2_N)

PHATRDRAFT_51604 - swi2 snf2-like protein (SNF2_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51604
PHATRDRAFT_54960 (SPFH_prohibitin)

PHATRDRAFT_54960 - (SPFH_prohibitin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54960
PHATRDRAFT_55086 delta-1-pyrroline 5-carboxylase synthetase (PLN02418)

PHATRDRAFT_55086 - delta-1-pyrroline 5-carboxylase synthetase (PLN02418)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55086
PHATRDRAFT_5512 alanine racemase family protein (PLPDE_III_YBL036c_euk)

PHATRDRAFT_5512 - alanine racemase family protein (PLPDE_III_YBL036c_euk)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5512
PHATRDRAFT_5902 heme oxygenase (HemeO)

PHATRDRAFT_5902 - heme oxygenase (HemeO)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5902
PHATRDRAFT_769 nuclear vcp-like protein (SpoVK)

PHATRDRAFT_769 - nuclear vcp-like protein (SpoVK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_769
PHATRDRAFT_8269 rnp-1 like rna-binding protein (RRM_SF superfamily)

PHATRDRAFT_8269 - rnp-1 like rna-binding protein (RRM_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8269
GO ID Go Term p-value q-value Cluster
GO:0006886 intracellular protein transport 0.204649 1 Phatr_bicluster_0024
GO:0009058 biosynthesis 0.227215 1 Phatr_bicluster_0024
GO:0006396 RNA processing 0.274724 1 Phatr_bicluster_0024
GO:0016567 protein ubiquitination 0.33887 1 Phatr_bicluster_0024
GO:0006118 electron transport 0.376784 1 Phatr_bicluster_0024
GO:0009306 protein secretion 0.01133 1 Phatr_bicluster_0024
GO:0006457 protein folding 0.491488 1 Phatr_bicluster_0024
GO:0006788 heme oxidation 0.0169488 1 Phatr_bicluster_0024
GO:0008152 metabolism 0.505893 1 Phatr_bicluster_0024
GO:0019856 pyrimidine base biosynthesis 0.0169488 1 Phatr_bicluster_0024
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