Phatr_bicluster_0104 Residual: 0.29
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_0104 0.29 Phaeodactylum tricornutum
Displaying 1 - 24 of 24
PHATRDRAFT_12538 related to ubiquitin fusion degradation protein 2 (U-box superfamily)

PHATRDRAFT_12538 - related to ubiquitin fusion degradation protein 2 (U-box superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12538
PHATRDRAFT_12578 pmt3_schpo ubiquitin-like protein pmt3 smt3 precursor (UBQ superfamily)

PHATRDRAFT_12578 - pmt3_schpo ubiquitin-like protein pmt3 smt3 precursor (UBQ superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12578
PHATRDRAFT_12583 manganese superoxide dismutase (SodA)

PHATRDRAFT_12583 - manganese superoxide dismutase (SodA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12583
PHATRDRAFT_14887 tkl family protein kinase (PKc_like superfamily)

PHATRDRAFT_14887 - tkl family protein kinase (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14887
PHATRDRAFT_17885 sec61p gamma subunit (SecE superfamily)

PHATRDRAFT_17885 - sec61p gamma subunit (SecE superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17885
PHATRDRAFT_19705 dolichol-phosphate mannosyltransferase (DPM1_like)

PHATRDRAFT_19705 - dolichol-phosphate mannosyltransferase (DPM1_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19705
PHATRDRAFT_23423 silicon transporter (Silic_transp superfamily)

PHATRDRAFT_23423 - silicon transporter (Silic_transp superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23423
PHATRDRAFT_27508 proteasomealpha type 1 (proteasome_alpha_type_1)

PHATRDRAFT_27508 - proteasomealpha type 1 (proteasome_alpha_type_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27508
PHATRDRAFT_32083 phosphatidic acid phosphatase-related pap2-related (PAP2_like superfamily)

PHATRDRAFT_32083 - phosphatidic acid phosphatase-related pap2-related (PAP2_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32083
PHATRDRAFT_33827 mitochondrial thiamine pyrophosphate transporter (Mito_carr)

PHATRDRAFT_33827 - mitochondrial thiamine pyrophosphate transporter (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33827
PHATRDRAFT_38413 epsilon frustilin

PHATRDRAFT_38413 - epsilon frustilin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38413
PHATRDRAFT_42659 nadh-flavin reductase (NADB_Rossmann superfamily)

PHATRDRAFT_42659 - nadh-flavin reductase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42659
PHATRDRAFT_43133 heat shock protein binding

PHATRDRAFT_43133 - heat shock protein binding

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43133
PHATRDRAFT_43489 helicase domain protein (HA)

PHATRDRAFT_43489 - helicase domain protein (HA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43489
PHATRDRAFT_44888 mate efflux family protein (MATE_like superfamily)

PHATRDRAFT_44888 - mate efflux family protein (MATE_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44888
PHATRDRAFT_44898

PHATRDRAFT_44898 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44898
PHATRDRAFT_45343 (Methyltransf_21)

PHATRDRAFT_45343 - (Methyltransf_21)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45343
PHATRDRAFT_45679 disease resistance protein

PHATRDRAFT_45679 - disease resistance protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45679
PHATRDRAFT_45966 cupin superfamily protein (COG2850)

PHATRDRAFT_45966 - cupin superfamily protein (COG2850)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45966
PHATRDRAFT_46005 cog4_dromeconserved oligomeric golgi complex component 4 (COG4 superfamily)

PHATRDRAFT_46005 - cog4_dromeconserved oligomeric golgi complex component 4 (COG4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46005
PHATRDRAFT_46440 novel proteinvertebrate nucleoporin 107kda (Nup84_Nup100 superfamily)

PHATRDRAFT_46440 - novel proteinvertebrate nucleoporin 107kda (Nup84_Nup100 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46440
PHATRDRAFT_47229

PHATRDRAFT_47229 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47229
PHATRDRAFT_48707 silicon transporter (Silic_transp superfamily)

PHATRDRAFT_48707 - silicon transporter (Silic_transp superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48707
PHATRDRAFT_55090 silicon transporter (Silic_transp superfamily)

PHATRDRAFT_55090 - silicon transporter (Silic_transp superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55090
GO ID Go Term p-value q-value Cluster
GO:0006855 multidrug transport 0.00984608 1 Phatr_bicluster_0104
GO:0006801 superoxide metabolism 0.00984608 1 Phatr_bicluster_0104
GO:0006605 protein targeting 0.0147363 1 Phatr_bicluster_0104
GO:0015031 protein transport 0.074057 1 Phatr_bicluster_0104
GO:0006886 intracellular protein transport 0.0946124 1 Phatr_bicluster_0104
GO:0006511 ubiquitin-dependent protein catabolism 0.105854 1 Phatr_bicluster_0104
GO:0006464 protein modification 0.14529 1 Phatr_bicluster_0104
GO:0016567 protein ubiquitination 0.164415 1 Phatr_bicluster_0104
GO:0006468 protein amino acid phosphorylation 0.352461 1 Phatr_bicluster_0104
GO:0006810 transport 0.38354 1 Phatr_bicluster_0104
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