Phatr_bicluster_0117 Residual: 0.31
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_0117 0.31 Phaeodactylum tricornutum
Displaying 1 - 29 of 29
PHATRDRAFT_12234 nucleotidyltransferase family protein (PAP_central)

PHATRDRAFT_12234 - nucleotidyltransferase family protein (PAP_central)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12234
PHATRDRAFT_13294 ribosomal large subunit pseudouridine synthase a (RluA)

PHATRDRAFT_13294 - ribosomal large subunit pseudouridine synthase a (RluA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13294
PHATRDRAFT_16065 shwachman-bodian-diamond syndrome (COG1500)

PHATRDRAFT_16065 - shwachman-bodian-diamond syndrome (COG1500)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16065
PHATRDRAFT_16155 yl92_schpo uncharacterized protein (PTZ00368)

PHATRDRAFT_16155 - yl92_schpo uncharacterized protein (PTZ00368)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16155
PHATRDRAFT_16560 3-5 exoribonuclease ph component of the exosome (RNase_PH superfamily)

PHATRDRAFT_16560 - 3-5 exoribonuclease ph component of the exosome (RNase_PH superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16560
PHATRDRAFT_18274 cyclophilin-like protein (cyclophilin_ABH_like)

PHATRDRAFT_18274 - cyclophilin-like protein (cyclophilin_ABH_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18274
PHATRDRAFT_19659 alcoholiron1 isoform 1 (HOT)

PHATRDRAFT_19659 - alcoholiron1 isoform 1 (HOT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19659
PHATRDRAFT_29958 u2 snrnp auxiliarysmall subunit (RRM_SF superfamily)

PHATRDRAFT_29958 - u2 snrnp auxiliarysmall subunit (RRM_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29958
PHATRDRAFT_31458

PHATRDRAFT_31458 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31458
PHATRDRAFT_3182 hect (homologous to the e6-apcarboxyl terminus) domain and rcc1-like domainpartial (RCC1)

PHATRDRAFT_3182 - hect (homologous to the e6-apcarboxyl terminus) domain and rcc1-like domainpartial (RCC1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3182
PHATRDRAFT_33524 cax-interacting protein 4-like

PHATRDRAFT_33524 - cax-interacting protein 4-like

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33524
PHATRDRAFT_33916

PHATRDRAFT_33916 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33916
PHATRDRAFT_37109 transmembrane efflux protein (ATG22)

PHATRDRAFT_37109 - transmembrane efflux protein (ATG22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37109
PHATRDRAFT_40731 amino acid permease-like protein (Aa_trans superfamily)

PHATRDRAFT_40731 - amino acid permease-like protein (Aa_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40731
PHATRDRAFT_43219

PHATRDRAFT_43219 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43219
PHATRDRAFT_43407

PHATRDRAFT_43407 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43407
PHATRDRAFT_45173 tpa: zinc finger protein (zf-DHHC)

PHATRDRAFT_45173 - tpa: zinc finger protein (zf-DHHC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45173
PHATRDRAFT_45199 serine arginine repetitive matrix 2 (PTZ00121)

PHATRDRAFT_45199 - serine arginine repetitive matrix 2 (PTZ00121)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45199
PHATRDRAFT_45412 (ZnMc superfamily)

PHATRDRAFT_45412 - (ZnMc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45412
PHATRDRAFT_45968 nucleosome binding protein (HMGB-UBF_HMG-box)

PHATRDRAFT_45968 - nucleosome binding protein (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45968
PHATRDRAFT_46061

PHATRDRAFT_46061 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46061
PHATRDRAFT_48350 (CHD)

PHATRDRAFT_48350 - (CHD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48350
PHATRDRAFT_5060 transcription factor dp-2 (e2f dimerization partner 2) (DP superfamily)

PHATRDRAFT_5060 - transcription factor dp-2 (e2f dimerization partner 2) (DP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5060
PHATRDRAFT_6032 diguanylate cyclase with gaf sensor (GAF)

PHATRDRAFT_6032 - diguanylate cyclase with gaf sensor (GAF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6032
PHATRDRAFT_6387 membrane family (SapB)

PHATRDRAFT_6387 - membrane family (SapB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6387
PHATRDRAFT_7007 ntp pyrophosphohydrolase (Nudix_Hydrolase superfamily)

PHATRDRAFT_7007 - ntp pyrophosphohydrolase (Nudix_Hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7007
PHATRDRAFT_7026 ck1 family protein kinase (PKc_like superfamily)

PHATRDRAFT_7026 - ck1 family protein kinase (PKc_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7026
PHATRDRAFT_8706 6-phosphofructo-2-kinase fructose--bisphosphatase short form (AAA_17 superfamily)

PHATRDRAFT_8706 - 6-phosphofructo-2-kinase fructose--bisphosphatase short form (AAA_17 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8706
PHATRDRAFT_8737 98b protein (HMGB-UBF_HMG-box)

PHATRDRAFT_8737 - 98b protein (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8737
GO ID Go Term p-value q-value Cluster
GO:0006003 fructose 2,6-bisphosphate metabolism 0.00887241 1 Phatr_bicluster_0117
GO:0006396 RNA processing 0.0249465 1 Phatr_bicluster_0117
GO:0006807 nitrogen compound metabolism 0.0605653 1 Phatr_bicluster_0117
GO:0006355 regulation of transcription, DNA-dependent 0.0698674 1 Phatr_bicluster_0117
GO:0009190 cyclic nucleotide biosynthesis 0.0730847 1 Phatr_bicluster_0117
GO:0006350 transcription 0.0895323 1 Phatr_bicluster_0117
GO:0006865 amino acid transport 0.117654 1 Phatr_bicluster_0117
GO:0000074 regulation of cell cycle 0.141104 1 Phatr_bicluster_0117
GO:0007242 intracellular signaling cascade 0.171456 1 Phatr_bicluster_0117
GO:0007165 signal transduction 0.189908 1 Phatr_bicluster_0117
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