Phatr_bicluster_0040 Residual: 0.38
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_0040 0.38 Phaeodactylum tricornutum
Displaying 1 - 50 of 50
PHATRDRAFT_12985 class i peptide chain release factor (PRK09256)

PHATRDRAFT_12985 - class i peptide chain release factor (PRK09256)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12985
PHATRDRAFT_13313 af375428_1at4g29590 t16l4_100 (Methyltransf_11)

PHATRDRAFT_13313 - af375428_1at4g29590 t16l4_100 (Methyltransf_11)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13313
PHATRDRAFT_16142 abc transporter related (Uup)

PHATRDRAFT_16142 - abc transporter related (Uup)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16142
PHATRDRAFT_16455 atpase aaa-2 (AAA)

PHATRDRAFT_16455 - atpase aaa-2 (AAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16455
PHATRDRAFT_16499 homoserine o-acetyltransferase (metX superfamily)

PHATRDRAFT_16499 - homoserine o-acetyltransferase (metX superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16499
PHATRDRAFT_20026 atp-bindingsub-family b (mdr tap)member 9 (MdlB)

PHATRDRAFT_20026 - atp-bindingsub-family b (mdr tap)member 9 (MdlB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20026
PHATRDRAFT_23247 cytosolic fructose--bisphosphatase (FBPase)

PHATRDRAFT_23247 - cytosolic fructose--bisphosphatase (FBPase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23247
PHATRDRAFT_29309 aminopeptidase n (pepN)

PHATRDRAFT_29309 - aminopeptidase n (pepN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29309
PHATRDRAFT_33947 gtp pyrophosphokinase (SpoT)

PHATRDRAFT_33947 - gtp pyrophosphokinase (SpoT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33947
PHATRDRAFT_36377

PHATRDRAFT_35089 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35089
PHATRDRAFT_36769 saccharopine dehydrogenase related protein

PHATRDRAFT_36377 - saccharopine dehydrogenase related protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36377
PHATRDRAFT_37363 (TRX_Fd_family)

PHATRDRAFT_36769 - (TRX_Fd_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36769
PHATRDRAFT_37367

PHATRDRAFT_37363 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37363
PHATRDRAFT_37514 beta-ketoacyl synthase (fabF)

PHATRDRAFT_37367 - beta-ketoacyl synthase (fabF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37367
PHATRDRAFT_37590

PHATRDRAFT_37514 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37514
PHATRDRAFT_37655 (zf-DNL superfamily)

PHATRDRAFT_37590 - (zf-DNL superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37590
PHATRDRAFT_38627 f-box only protein 31 (DUF3506 superfamily)

PHATRDRAFT_37655 - f-box only protein 31 (DUF3506 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37655
PHATRDRAFT_40135

PHATRDRAFT_38627 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38627
PHATRDRAFT_40354 saccharopine dehydrogenase related protein (LYS9)

PHATRDRAFT_40135 - saccharopine dehydrogenase related protein (LYS9)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40135
PHATRDRAFT_40996

PHATRDRAFT_40354 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40354
PHATRDRAFT_42247

PHATRDRAFT_40996 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40996
PHATRDRAFT_42565 asparaginyl-trna synthetase (asnC)

PHATRDRAFT_42247 - asparaginyl-trna synthetase (asnC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42247
PHATRDRAFT_42835 peroxisomal membrane protein mpv17 and related proteins (Mpv17_PMP22)

PHATRDRAFT_42565 - peroxisomal membrane protein mpv17 and related proteins (Mpv17_PMP22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42565
PHATRDRAFT_43270 (NADB_Rossmann superfamily)

PHATRDRAFT_42835 - (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42835
PHATRDRAFT_44692 (LPA1)

PHATRDRAFT_43270 - (LPA1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43270
PHATRDRAFT_44884 (Ubiq_cyt_C_chap)

PHATRDRAFT_44692 - (Ubiq_cyt_C_chap)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44692
PHATRDRAFT_45443 chitinase (Glyco_hydro_18)

PHATRDRAFT_44884 - chitinase (Glyco_hydro_18)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44884
PHATRDRAFT_45544 carbonic anhydrase family protein (beta_CA_cladeA)

PHATRDRAFT_45443 - carbonic anhydrase family protein (beta_CA_cladeA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45443
PHATRDRAFT_45918 myosin heavy chain

PHATRDRAFT_45544 - myosin heavy chain

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45544
PHATRDRAFT_46071 short chain dehydrogenase reductase family protein (NADB_Rossmann superfamily)

PHATRDRAFT_45918 - short chain dehydrogenase reductase family protein (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45918
PHATRDRAFT_46303 (DUF3007)

PHATRDRAFT_46071 - (DUF3007)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46071
PHATRDRAFT_46415

PHATRDRAFT_46303 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46303
PHATRDRAFT_47423

PHATRDRAFT_46415 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46415
PHATRDRAFT_47593 atp-dependent zn proteases-like protein

PHATRDRAFT_47423 - atp-dependent zn proteases-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47423
PHATRDRAFT_48099 faceless pollen-1 (PLN02869)

PHATRDRAFT_47593 - faceless pollen-1 (PLN02869)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47593
PHATRDRAFT_48359

PHATRDRAFT_48099 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48099
PHATRDRAFT_48423 photosystem ii oxygen evolving complex protein (PsbP superfamily)

PHATRDRAFT_48359 - photosystem ii oxygen evolving complex protein (PsbP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48359
PHATRDRAFT_49022 delta 12 fatty acid desaturase (Delta12-FADS-like)

PHATRDRAFT_48423 - delta 12 fatty acid desaturase (Delta12-FADS-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48423
PHATRDRAFT_49981

PHATRDRAFT_49022 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49022
PHATRDRAFT_49990 (2OG-FeII_Oxy_2)

PHATRDRAFT_49981 - (2OG-FeII_Oxy_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49981
PHATRDRAFT_50443

PHATRDRAFT_49990 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49990
PHATRDRAFT_50512 delta8 fatty acid desaturase-like protein (Delta6-FADS-like)

PHATRDRAFT_50443 - delta8 fatty acid desaturase-like protein (Delta6-FADS-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50443
PHATRDRAFT_50542 novel protein

PHATRDRAFT_50512 - novel protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50512
PHATRDRAFT_50546 mitochondrial substrate carrier protein (Mito_carr)

PHATRDRAFT_50542 - mitochondrial substrate carrier protein (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50542
PHATRDRAFT_5271 (PPR_2)

PHATRDRAFT_50546 - (PPR_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50546
PHATRDRAFT_54982 low co2-induced protein (Kua-UEV1_localn superfamily)

PHATRDRAFT_5271 - low co2-induced protein (Kua-UEV1_localn superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5271
PHATRDRAFT_55157 respiratory burst oxidase-like protein (NOX_Duox_like_FAD_NADP)

PHATRDRAFT_54982 - respiratory burst oxidase-like protein (NOX_Duox_like_FAD_NADP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54982
PHATRDRAFT_9040 beta-hydroxyacyl-acp dehydratase precursor (FabZ)

PHATRDRAFT_55157 - beta-hydroxyacyl-acp dehydratase precursor (FabZ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55157
PHATRDRAFT_9654 zeta-carotene desaturase (zeta_caro_desat)

PHATRDRAFT_9040 - zeta-carotene desaturase (zeta_caro_desat)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9040

PHATRDRAFT_9654 - histidinol dehydrogenase (hisD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9654
GO ID Go Term p-value q-value Cluster
GO:0006421 asparaginyl-tRNA aminoacylation 0.0108387 1 Phatr_bicluster_0040
GO:0006422 aspartyl-tRNA aminoacylation 0.0321806 1 Phatr_bicluster_0040
GO:0005975 carbohydrate metabolism 0.292419 1 Phatr_bicluster_0040
GO:0015976 carbon utilization 0.0108387 1 Phatr_bicluster_0040
GO:0006260 DNA replication 0.132461 1 Phatr_bicluster_0040
GO:0006118 electron transport 0.723145 1 Phatr_bicluster_0040
GO:0006633 fatty acid biosynthesis 0.0684755 1 Phatr_bicluster_0040
GO:0006636 fatty acid desaturation 0.00123541 1 Phatr_bicluster_0040
GO:0015969 guanosine tetraphosphate metabolism 0.0108387 1 Phatr_bicluster_0040
GO:0000105 histidine biosynthesis 0.0478978 1 Phatr_bicluster_0040
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