Phatr_bicluster_0083 Residual: 0.30
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_0083 0.30 Phaeodactylum tricornutum
Displaying 1 - 33 of 33
PHATRDRAFT_12312 atp-dependent rna helicase (HELICc)

PHATRDRAFT_12312 - atp-dependent rna helicase (HELICc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12312
PHATRDRAFT_13752 mitochondrial carrier protein (Mito_carr)

PHATRDRAFT_13752 - mitochondrial carrier protein (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13752
PHATRDRAFT_14138 trna (guanine-n-)-methyltransferase (Methyltransf_4 superfamily)

PHATRDRAFT_14138 - trna (guanine-n-)-methyltransferase (Methyltransf_4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14138
PHATRDRAFT_19122 dimethyladenosine transferase (AdoMet_MTases)

PHATRDRAFT_19122 - dimethyladenosine transferase (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19122
PHATRDRAFT_20342 nadh-glutamate synthase small chain (gltD)

PHATRDRAFT_20342 - nadh-glutamate synthase small chain (gltD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20342
PHATRDRAFT_3131 (Ras_like_GTPase superfamily)

PHATRDRAFT_3131 - (Ras_like_GTPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3131
PHATRDRAFT_32139 (Nop16 superfamily)

PHATRDRAFT_32139 - (Nop16 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32139
PHATRDRAFT_32588

PHATRDRAFT_32588 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32588
PHATRDRAFT_38166

PHATRDRAFT_38166 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38166
PHATRDRAFT_38548

PHATRDRAFT_38548 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38548
PHATRDRAFT_41091 (DUF2039 superfamily)

PHATRDRAFT_41091 - (DUF2039 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41091
PHATRDRAFT_41785 eukaryotic initiation factor (PTZ00424)

PHATRDRAFT_41785 - eukaryotic initiation factor (PTZ00424)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41785
PHATRDRAFT_42428 rna binding s1 (COG2996)

PHATRDRAFT_42428 - rna binding s1 (COG2996)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42428
PHATRDRAFT_43322

PHATRDRAFT_43322 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43322
PHATRDRAFT_43323

PHATRDRAFT_43323 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43323
PHATRDRAFT_45079 diacylglycerol kinase (LCB5)

PHATRDRAFT_45079 - diacylglycerol kinase (LCB5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45079
PHATRDRAFT_45542

PHATRDRAFT_45542 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45542
PHATRDRAFT_46371 methyltransfer with n-terminal ankyrin repeats (ANK)

PHATRDRAFT_46371 - methyltransfer with n-terminal ankyrin repeats (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46371
PHATRDRAFT_46452

PHATRDRAFT_46452 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46452
PHATRDRAFT_46453 arystal structure of human choline kinase alpha 2 (APH_ChoK_like superfamily)

PHATRDRAFT_46453 - arystal structure of human choline kinase alpha 2 (APH_ChoK_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46453
PHATRDRAFT_46888

PHATRDRAFT_46888 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46888
PHATRDRAFT_46999 deoxyhypusine synthase (DS)

PHATRDRAFT_46999 - deoxyhypusine synthase (DS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46999
PHATRDRAFT_47017 mms19l-prov protein (MMS19_N superfamily)

PHATRDRAFT_47017 - mms19l-prov protein (MMS19_N superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47017
PHATRDRAFT_47242 (MFS_2)

PHATRDRAFT_47242 - (MFS_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47242
PHATRDRAFT_47613 (Methyltransf_32 superfamily)

PHATRDRAFT_47613 - (Methyltransf_32 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47613
PHATRDRAFT_48912 c2h2 finger domain

PHATRDRAFT_48912 - c2h2 finger domain

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48912
PHATRDRAFT_49518

PHATRDRAFT_49518 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49518
PHATRDRAFT_49908 mus musculushomolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (DnaJ)

PHATRDRAFT_49908 - mus musculushomolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49908
PHATRDRAFT_50053

PHATRDRAFT_50053 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50053
PHATRDRAFT_54092 myb domain-containing protein (SWIRM)

PHATRDRAFT_54092 - myb domain-containing protein (SWIRM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54092
PHATRDRAFT_6934 myo-inositol-1-phosphate synthase family protein (NAD_binding_5 superfamily)

PHATRDRAFT_6934 - myo-inositol-1-phosphate synthase family protein (NAD_binding_5 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6934
PHATRDRAFT_7634 dusp12 protein

PHATRDRAFT_7634 - dusp12 protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7634
PHATRDRAFT_9283 nadph-cytochrome p450 oxidoreductase (CysJ)

PHATRDRAFT_9283 - nadph-cytochrome p450 oxidoreductase (CysJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9283
GO ID Go Term p-value q-value Cluster
GO:0008612 hypusine biosynthesis from peptidyl-lysine 0.00296369 1 Phatr_bicluster_0083
GO:0050983 spermidine catabolism to deoxyhypusine, using deoxyhypusine synthase 0.00296369 1 Phatr_bicluster_0083
GO:0000154 rRNA modification 0.00591934 1 Phatr_bicluster_0083
GO:0007205 protein kinase C activation 0.00886694 1 Phatr_bicluster_0083
GO:0006537 glutamate biosynthesis 0.0147381 1 Phatr_bicluster_0083
GO:0006364 rRNA processing 0.0234852 1 Phatr_bicluster_0083
GO:0006118 electron transport 0.144823 1 Phatr_bicluster_0083
GO:0005975 carbohydrate metabolism 0.171749 1 Phatr_bicluster_0083
GO:0016567 protein ubiquitination 0.193944 1 Phatr_bicluster_0083
GO:0006457 protein folding 0.296964 1 Phatr_bicluster_0083
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