Phatr_bicluster_0012 Residual: 0.51
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_0012 0.51 Phaeodactylum tricornutum
Displaying 1 - 41 of 41
PHATRDRAFT_14403 sodium hydrogen exchanger8 (TM_PBP1_branched-chain-AA_like superfamily)

PHATRDRAFT_14403 - sodium hydrogen exchanger8 (TM_PBP1_branched-chain-AA_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14403
PHATRDRAFT_25769 delta 12 fatty acid desaturase (Delta12-FADS-like)

PHATRDRAFT_25769 - delta 12 fatty acid desaturase (Delta12-FADS-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25769
PHATRDRAFT_29532 immunoglobulin mu binding protein 2 (AAA_12)

PHATRDRAFT_29532 - immunoglobulin mu binding protein 2 (AAA_12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29532
PHATRDRAFT_33457

PHATRDRAFT_33457 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33457
PHATRDRAFT_33641

PHATRDRAFT_33641 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33641
PHATRDRAFT_3730 protein kinase family member (kin-1) (PKc_like superfamily)

PHATRDRAFT_3730 - protein kinase family member (kin-1) (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3730
PHATRDRAFT_38016 c-terminal zinc-finger (RING)

PHATRDRAFT_38016 - c-terminal zinc-finger (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38016
PHATRDRAFT_38149 aaa+-type atpase (DUF1995 superfamily)

PHATRDRAFT_38149 - aaa+-type atpase (DUF1995 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38149
PHATRDRAFT_38186

PHATRDRAFT_38186 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38186
PHATRDRAFT_38772

PHATRDRAFT_38772 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38772
PHATRDRAFT_38886 cell division cycle protein 23-like protein (APC8 superfamily)

PHATRDRAFT_38886 - cell division cycle protein 23-like protein (APC8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38886
PHATRDRAFT_39556 (Rhamno_transf superfamily)

PHATRDRAFT_39556 - (Rhamno_transf superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39556
PHATRDRAFT_39797 ahe x-ray crystal structure of ferric synechocystis hemoglobin h117a mutant with a covalent linkage (globin_like superfamily)

PHATRDRAFT_39797 - ahe x-ray crystal structure of ferric synechocystis hemoglobin h117a mutant with a covalent linkage (globin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39797
PHATRDRAFT_40538

PHATRDRAFT_40538 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40538
PHATRDRAFT_40744 secreted metalloprotease (Peptidase_M6 superfamily)

PHATRDRAFT_40744 - secreted metalloprotease (Peptidase_M6 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40744
PHATRDRAFT_41418 cg12788-isoform a (selen_PSTK_euk superfamily)

PHATRDRAFT_41418 - cg12788-isoform a (selen_PSTK_euk superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41418
PHATRDRAFT_41510

PHATRDRAFT_41510 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41510
PHATRDRAFT_42882

PHATRDRAFT_42882 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42882
PHATRDRAFT_43419 nhp6_klula non-histone chromosomal protein 6 (HMGB-UBF_HMG-box)

PHATRDRAFT_43419 - nhp6_klula non-histone chromosomal protein 6 (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43419
PHATRDRAFT_44088

PHATRDRAFT_44088 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44088
PHATRDRAFT_44394 riken cdna 2600005c20isoform cra_b (Nop52 superfamily)

PHATRDRAFT_44394 - riken cdna 2600005c20isoform cra_b (Nop52 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44394
PHATRDRAFT_46177

PHATRDRAFT_46177 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46177
PHATRDRAFT_46301

PHATRDRAFT_46301 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46301
PHATRDRAFT_46381

PHATRDRAFT_46381 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46381
PHATRDRAFT_47528

PHATRDRAFT_47528 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47528
PHATRDRAFT_47888 glycosidefamily 6

PHATRDRAFT_47888 - glycosidefamily 6

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47888
PHATRDRAFT_48106 octopine dehydrogenase (Octopine_DH superfamily)

PHATRDRAFT_48106 - octopine dehydrogenase (Octopine_DH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48106
PHATRDRAFT_48169

PHATRDRAFT_48169 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48169
PHATRDRAFT_48511 chromate transporter (2A51)

PHATRDRAFT_48511 - chromate transporter (2A51)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48511
PHATRDRAFT_48697 (DUF563)

PHATRDRAFT_48697 - (DUF563)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48697
PHATRDRAFT_49121

PHATRDRAFT_49121 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49121
PHATRDRAFT_49145

PHATRDRAFT_49145 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49145
PHATRDRAFT_49150 (Nucleotid_trans superfamily)

PHATRDRAFT_49150 - (Nucleotid_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49150
PHATRDRAFT_49318

PHATRDRAFT_49318 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49318
PHATRDRAFT_49326

PHATRDRAFT_49326 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49326
PHATRDRAFT_49424

PHATRDRAFT_49424 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49424
PHATRDRAFT_49591 sulfide-quinone reductase

PHATRDRAFT_49591 - sulfide-quinone reductase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49591
PHATRDRAFT_49794

PHATRDRAFT_49794 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49794
PHATRDRAFT_49984

PHATRDRAFT_49984 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49984
PHATRDRAFT_50362 zinc finger protein 500

PHATRDRAFT_50362 - zinc finger protein 500

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50362
PHATRDRAFT_53961 cell wall surface anchor family protein

PHATRDRAFT_53961 - cell wall surface anchor family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_53961
GO ID Go Term p-value q-value Cluster
GO:0015703 chromate transport 0.00321067 1 Phatr_bicluster_0012
GO:0030071 regulation of mitotic metaphase/anaphase transition 0.00641182 1 Phatr_bicluster_0012
GO:0015671 oxygen transport 0.0127857 1 Phatr_bicluster_0012
GO:0006885 regulation of pH 0.0254203 1 Phatr_bicluster_0012
GO:0006364 rRNA processing 0.0254203 1 Phatr_bicluster_0012
GO:0006636 fatty acid desaturation 0.0316815 1 Phatr_bicluster_0012
GO:0006814 sodium ion transport 0.0347981 1 Phatr_bicluster_0012
GO:0006414 translational elongation 0.0440926 1 Phatr_bicluster_0012
GO:0006355 regulation of transcription, DNA-dependent 0.153654 1 Phatr_bicluster_0012
GO:0016567 protein ubiquitination 0.20832 1 Phatr_bicluster_0012
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