Phatr_bicluster_0160 Residual: 0.36
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_0160 0.36 Phaeodactylum tricornutum
Displaying 1 - 25 of 25
PHATRDRAFT_10029 splicing factor u2af large subunit (RRM3_U2AF65)

PHATRDRAFT_10029 - splicing factor u2af large subunit (RRM3_U2AF65)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10029
PHATRDRAFT_12322 exosome component 6 (RNase_PH superfamily)

PHATRDRAFT_12322 - exosome component 6 (RNase_PH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12322
PHATRDRAFT_13424 heat shock protein (PRK14293)

PHATRDRAFT_13424 - heat shock protein (PRK14293)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13424
PHATRDRAFT_13931 ke2 familyexpressed (Prefoldin_2)

PHATRDRAFT_13931 - ke2 familyexpressed (Prefoldin_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13931
PHATRDRAFT_16766 3-5-exoribonuclease rna binding (RNase_PH superfamily)

PHATRDRAFT_16766 - 3-5-exoribonuclease rna binding (RNase_PH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16766
PHATRDRAFT_22325 htransporter (pgp related) family member (haf-4) (MdlB)

PHATRDRAFT_22325 - htransporter (pgp related) family member (haf-4) (MdlB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22325
PHATRDRAFT_26363 hypothetical isochorismatase family protein (cysteine_hydrolases)

PHATRDRAFT_26363 - hypothetical isochorismatase family protein (cysteine_hydrolases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26363
PHATRDRAFT_27263 protein c14orf111 (PIN_Fcf1)

PHATRDRAFT_27263 - protein c14orf111 (PIN_Fcf1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27263
PHATRDRAFT_34050 g-patch domain containing protein (G_patch)

PHATRDRAFT_34050 - g-patch domain containing protein (G_patch)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34050
PHATRDRAFT_35396 (CHORD superfamily)

PHATRDRAFT_35396 - (CHORD superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35396
PHATRDRAFT_39304 uvb-resistance protein uvr8 (RCC1)

PHATRDRAFT_39304 - uvb-resistance protein uvr8 (RCC1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39304
PHATRDRAFT_42302 methyltransferase wbscr22 (williams-beuren syndrome chromosome region 22 protein homolog) (WBS_methylT)

PHATRDRAFT_42302 - methyltransferase wbscr22 (williams-beuren syndrome chromosome region 22 protein homolog) (WBS_methylT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42302
PHATRDRAFT_42307 translation initiation factor 2 gamma subunit (PTZ00327)

PHATRDRAFT_42307 - translation initiation factor 2 gamma subunit (PTZ00327)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42307
PHATRDRAFT_42831 ribosome biogenesis protein bms1 homolog (BMS1)

PHATRDRAFT_42831 - ribosome biogenesis protein bms1 homolog (BMS1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42831
PHATRDRAFT_43528

PHATRDRAFT_43528 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43528
PHATRDRAFT_43677 ribonuclease ii (RNB)

PHATRDRAFT_43677 - ribonuclease ii (RNB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43677
PHATRDRAFT_43713 u3 small nucleolarhomolog (UTP15_C)

PHATRDRAFT_43713 - u3 small nucleolarhomolog (UTP15_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43713
PHATRDRAFT_44072

PHATRDRAFT_44072 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44072
PHATRDRAFT_47222

PHATRDRAFT_47222 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47222
PHATRDRAFT_47726 chaperone protein (ZUO1)

PHATRDRAFT_47726 - chaperone protein (ZUO1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47726
PHATRDRAFT_47728 zuotin related factor 1 (SANT)

PHATRDRAFT_47728 - zuotin related factor 1 (SANT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47728
PHATRDRAFT_49146 -like family protein zinc finger (ccch-type) family protein (CwfJ_C_1 superfamily)

PHATRDRAFT_49146 - -like family protein zinc finger (ccch-type) family protein (CwfJ_C_1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49146
PHATRDRAFT_49881

PHATRDRAFT_49881 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49881
PHATRDRAFT_51460 spermine synthase (AdoMet_MTases)

PHATRDRAFT_51460 - spermine synthase (AdoMet_MTases)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51460

PHATRDRAFT_7923 - zinc finger protein (zf-C2H2_jaz superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7923
GO ID Go Term p-value q-value Cluster
GO:0006396 RNA processing 0.00377412 1 Phatr_bicluster_0160
GO:0006457 protein folding 0.01581 1 Phatr_bicluster_0160
GO:0006412 protein biosynthesis 0.247414 1 Phatr_bicluster_0160
GO:0006810 transport 0.287164 1 Phatr_bicluster_0160
GO:0008152 metabolism 0.410263 1 Phatr_bicluster_0160
Log in to post comments