Phatr_bicluster_0091 Residual: 0.41
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_0091 0.41 Phaeodactylum tricornutum
Displaying 1 - 47 of 47
PHATRDRAFT_15324 amino acid permease familyexpressed (2A0303)

PHATRDRAFT_15324 - amino acid permease familyexpressed (2A0303)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15324
PHATRDRAFT_22739 solute carrier family 35 (udp-n-acetylglucosamine (udp-c) transporter)member 3 (Nuc_sug_transp)

PHATRDRAFT_22739 - solute carrier family 35 (udp-n-acetylglucosamine (udp-c) transporter)member 3 (Nuc_sug_transp)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22739
PHATRDRAFT_29608 cg1109-isoform a (WD40)

PHATRDRAFT_29608 - cg1109-isoform a (WD40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29608
PHATRDRAFT_29660 nadh-cytochrome b-5 reductase (cyt_b5_reduct_like)

PHATRDRAFT_29660 - nadh-cytochrome b-5 reductase (cyt_b5_reduct_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29660
PHATRDRAFT_31160 member ras oncogene family (Rab11_like)

PHATRDRAFT_31160 - member ras oncogene family (Rab11_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31160
PHATRDRAFT_32178 nuclear division rft1 (MATE_like superfamily)

PHATRDRAFT_32178 - nuclear division rft1 (MATE_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32178
PHATRDRAFT_33579

PHATRDRAFT_33579 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33579
PHATRDRAFT_34225

PHATRDRAFT_34225 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34225
PHATRDRAFT_37086 dictyostelium discoideum (slime mold) (CDP-OH_P_transf superfamily)

PHATRDRAFT_37086 - dictyostelium discoideum (slime mold) (CDP-OH_P_transf superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37086
PHATRDRAFT_37687

PHATRDRAFT_37687 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37687
PHATRDRAFT_37723 dna polymerase delta small subunit (MPP_superfamily superfamily)

PHATRDRAFT_37723 - dna polymerase delta small subunit (MPP_superfamily superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37723
PHATRDRAFT_37858 homogentisate phytyltransferase vte2-1 (PT_UbiA_HPT1)

PHATRDRAFT_37858 - homogentisate phytyltransferase vte2-1 (PT_UbiA_HPT1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37858
PHATRDRAFT_38196 gdsl-motif lipase hydrolase family protein (Isoamyl_acetate_hydrolase_like)

PHATRDRAFT_38196 - gdsl-motif lipase hydrolase family protein (Isoamyl_acetate_hydrolase_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38196
PHATRDRAFT_38686 phosphate translocator-related (TPT superfamily)

PHATRDRAFT_38686 - phosphate translocator-related (TPT superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38686
PHATRDRAFT_38866

PHATRDRAFT_38866 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38866
PHATRDRAFT_39173 domain protein (DnaJ)

PHATRDRAFT_39173 - domain protein (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39173
PHATRDRAFT_39417

PHATRDRAFT_39417 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39417
PHATRDRAFT_39457 extradiol ring-cleavageclass iiisubunit b (ED_3B_like)

PHATRDRAFT_39457 - extradiol ring-cleavageclass iiisubunit b (ED_3B_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39457
PHATRDRAFT_40176 cog0406: fructose--bisphosphatase (HP_PGM_like)

PHATRDRAFT_40176 - cog0406: fructose--bisphosphatase (HP_PGM_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40176
PHATRDRAFT_40425

PHATRDRAFT_40425 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40425
PHATRDRAFT_40441

PHATRDRAFT_40441 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40441
PHATRDRAFT_40863 hect domain and rldisoform cra_b

PHATRDRAFT_40863 - hect domain and rldisoform cra_b

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40863
PHATRDRAFT_41088 nad-dependent epimerase dehydratase (NADB_Rossmann superfamily)

PHATRDRAFT_41088 - nad-dependent epimerase dehydratase (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41088
PHATRDRAFT_41327 coated vesicle membrane protein (EMP24_GP25L)

PHATRDRAFT_41327 - coated vesicle membrane protein (EMP24_GP25L)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41327
PHATRDRAFT_43900 (DUF1620)

PHATRDRAFT_43900 - (DUF1620)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43900
PHATRDRAFT_44239 loc100049152 protein

PHATRDRAFT_44239 - loc100049152 protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44239
PHATRDRAFT_44596 nadh dehydrogenase

PHATRDRAFT_44596 - nadh dehydrogenase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44596
PHATRDRAFT_44662

PHATRDRAFT_44662 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44662
PHATRDRAFT_45072 helicase-like transcription factor hltf dna helicasedead-box superfamily (Dcm)

PHATRDRAFT_45072 - helicase-like transcription factor hltf dna helicasedead-box superfamily (Dcm)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45072
PHATRDRAFT_47916

PHATRDRAFT_47916 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47916
PHATRDRAFT_48059 ca2+-dependent lipid-binding (COG5038)

PHATRDRAFT_48059 - ca2+-dependent lipid-binding (COG5038)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48059
PHATRDRAFT_48083

PHATRDRAFT_48083 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48083
PHATRDRAFT_48287 glycosylfamily 2 (Glyco_tranf_GTA_type superfamily)

PHATRDRAFT_48287 - glycosylfamily 2 (Glyco_tranf_GTA_type superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48287
PHATRDRAFT_48677

PHATRDRAFT_48677 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48677
PHATRDRAFT_48930 e2f transcription factor 7 (E2F_TDP)

PHATRDRAFT_48930 - e2f transcription factor 7 (E2F_TDP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48930
PHATRDRAFT_49071 (COG1835)

PHATRDRAFT_49071 - (COG1835)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49071
PHATRDRAFT_49442 (ARM)

PHATRDRAFT_49442 - (ARM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49442
PHATRDRAFT_49480 epsilon-trimethyllysine 2-oxoglutarate dioxygenase (carnitine_bodg)

PHATRDRAFT_49480 - epsilon-trimethyllysine 2-oxoglutarate dioxygenase (carnitine_bodg)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49480
PHATRDRAFT_49523 response regulator receiver domain protein (-like) (P4Hc)

PHATRDRAFT_49523 - response regulator receiver domain protein (-like) (P4Hc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49523
PHATRDRAFT_49812

PHATRDRAFT_49812 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49812
PHATRDRAFT_50495 yjd1_schpo uncharacterized protein

PHATRDRAFT_50495 - yjd1_schpo uncharacterized protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50495
PHATRDRAFT_52561 mcm8 minichromosome maintenance deficient 8 (MCM)

PHATRDRAFT_52561 - mcm8 minichromosome maintenance deficient 8 (MCM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52561
PHATRDRAFT_54192 structural maintenance of chromosomes 5 (Smc)

PHATRDRAFT_54192 - structural maintenance of chromosomes 5 (Smc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54192
PHATRDRAFT_54992 polypeptide 1 (AE_Prim_S)

PHATRDRAFT_54992 - polypeptide 1 (AE_Prim_S)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54992
PHATRDRAFT_7649 histone acetyltransferase hpa2 related acetyltransferase (NAT_SF)

PHATRDRAFT_7649 - histone acetyltransferase hpa2 related acetyltransferase (NAT_SF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7649
PHATRDRAFT_8659 adp-ribosylation factor 3 (Arl1)

PHATRDRAFT_8659 - adp-ribosylation factor 3 (Arl1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8659
PHATRDRAFT_8835 chloroplast lycopene beta cyclase precursor (NAD_binding_8 superfamily)

PHATRDRAFT_8835 - chloroplast lycopene beta cyclase precursor (NAD_binding_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8835
GO ID Go Term p-value q-value Cluster
GO:0007264 small GTPase mediated signal transduction 0.00415482 1 Phatr_bicluster_0091
GO:0015031 protein transport 0.00894654 1 Phatr_bicluster_0091
GO:0006886 intracellular protein transport 0.0146352 1 Phatr_bicluster_0091
GO:0015780 nucleotide-sugar transport 0.0186452 1 Phatr_bicluster_0091
GO:0008654 phospholipid biosynthesis 0.0414888 1 Phatr_bicluster_0091
GO:0008643 carbohydrate transport 0.0726248 1 Phatr_bicluster_0091
GO:0006306 DNA methylation 0.0899841 1 Phatr_bicluster_0091
GO:0000160 two-component signal transduction system (phosphorelay) 0.115447 1 Phatr_bicluster_0091
GO:0006865 amino acid transport 0.123783 1 Phatr_bicluster_0091
GO:0000074 regulation of cell cycle 0.148349 1 Phatr_bicluster_0091
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