Phatr_bicluster_0176 Residual: 0.24
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_0176 0.24 Phaeodactylum tricornutum
Displaying 1 - 24 of 24
PHATRDRAFT_12310 snf2 domain-containing protein helicase domain-containing protein ring finger domain-containing protein (HepA)

PHATRDRAFT_12310 - snf2 domain-containing protein helicase domain-containing protein ring finger domain-containing protein (HepA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12310
PHATRDRAFT_16286 glucosamine-fructose-6-phosphate aminotransferase (PTZ00295)

PHATRDRAFT_14994 - glucosamine-fructose-6-phosphate aminotransferase (PTZ00295)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14994
PHATRDRAFT_25506 mitochondrial carrier (PTZ00169)

PHATRDRAFT_16286 - mitochondrial carrier (PTZ00169)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16286
PHATRDRAFT_28445 structural maintenance of chromosomes 1 protein (Smc)

PHATRDRAFT_25506 - structural maintenance of chromosomes 1 protein (Smc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25506
PHATRDRAFT_29196 h2a histoneprobable (H2A)

PHATRDRAFT_28445 - h2a histoneprobable (H2A)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28445
PHATRDRAFT_29283 proliferating cell nuclear antigen (PLN00057)

PHATRDRAFT_29196 - proliferating cell nuclear antigen (PLN00057)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29196
PHATRDRAFT_32557 cyclin j (CYCLIN)

PHATRDRAFT_29283 - cyclin j (CYCLIN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29283
PHATRDRAFT_33206 cg4050-isoform a (DUF1736 superfamily)

PHATRDRAFT_32557 - cg4050-isoform a (DUF1736 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32557
PHATRDRAFT_37466 timeout timeless-2 (TIMELESS superfamily)

PHATRDRAFT_33206 - timeout timeless-2 (TIMELESS superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33206
PHATRDRAFT_39306 nad dependent epimerase dehydratase family protein (NADB_Rossmann superfamily)

PHATRDRAFT_37466 - nad dependent epimerase dehydratase family protein (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37466
PHATRDRAFT_39374 ribonucleoside-diphosphatebeta subunit (RNRR2)

PHATRDRAFT_39306 - ribonucleoside-diphosphatebeta subunit (RNRR2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39306
PHATRDRAFT_42697 family exonuclease (Cas4_I-A_I-B_I-C_I-D_II-B superfamily)

PHATRDRAFT_39374 - family exonuclease (Cas4_I-A_I-B_I-C_I-D_II-B superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39374
PHATRDRAFT_42726

PHATRDRAFT_42697 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42697
PHATRDRAFT_44338 ribonucleoside-diphosphate reductase large chain (PLN02437)

PHATRDRAFT_42726 - ribonucleoside-diphosphate reductase large chain (PLN02437)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42726
PHATRDRAFT_44474 protein with potential galactosyl transferase activity (Glyco_transf_34 superfamily)

PHATRDRAFT_44338 - protein with potential galactosyl transferase activity (Glyco_transf_34 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44338
PHATRDRAFT_45690 p-type atpase (ATPase-IIB_Ca)

PHATRDRAFT_44474 - p-type atpase (ATPase-IIB_Ca)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44474
PHATRDRAFT_46806 sister chromatid cohesion-related protein (AAA)

PHATRDRAFT_45690 - sister chromatid cohesion-related protein (AAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45690
PHATRDRAFT_47152 dna primase large subunit (PriL_PriS_Eukaryotic)

PHATRDRAFT_46806 - dna primase large subunit (PriL_PriS_Eukaryotic)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46806
PHATRDRAFT_48436 rhamnose biosynthetic enzymeexpressed (dTDP_GD_SDR_e)

PHATRDRAFT_47152 - rhamnose biosynthetic enzymeexpressed (dTDP_GD_SDR_e)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47152
PHATRDRAFT_51597 fibrocystin-l-like protein

PHATRDRAFT_48436 - fibrocystin-l-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48436
PHATRDRAFT_53969 mini-chromosome maintenance protein mcm3 (MCM)

PHATRDRAFT_51597 - mini-chromosome maintenance protein mcm3 (MCM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51597
PHATRDRAFT_7646 (MutS)

PHATRDRAFT_53969 - (MutS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_53969
PHATRDRAFT_9344 deoxyuridine 5-triphosphateexpressed (trimeric_dUTPase)

PHATRDRAFT_7646 - deoxyuridine 5-triphosphateexpressed (trimeric_dUTPase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7646

PHATRDRAFT_9344 - cdc45 (cell division cycle 45) (CDC45 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9344
GO ID Go Term p-value q-value Cluster
GO:0046080 dUTP metabolism 0.00543344 1 Phatr_bicluster_0176
GO:0006275 regulation of DNA replication 0.00543344 1 Phatr_bicluster_0176
GO:0007585 respiratory gaseous exchange 0.00543344 1 Phatr_bicluster_0176
GO:0006260 DNA replication 0.0084651 1 Phatr_bicluster_0176
GO:0006269 DNA replication, synthesis of RNA primer 0.0108387 1 Phatr_bicluster_0176
GO:0000074 regulation of cell cycle 0.0142338 1 Phatr_bicluster_0176
GO:0006816 calcium ion transport 0.0162159 1 Phatr_bicluster_0176
GO:0009186 deoxyribonucleoside diphosphate metabolism 0.0162159 1 Phatr_bicluster_0176
GO:0051276 chromosome organization and biogenesis 0.0215652 1 Phatr_bicluster_0176
GO:0006270 DNA replication initiation 0.0321806 1 Phatr_bicluster_0176
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