Phatr_bicluster_0148 Residual: 0.35
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_0148 0.35 Phaeodactylum tricornutum
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Displaying 1 - 33 of 33
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PHATRDRAFT_10024 heterogeneous nuclear ribonucleoprotein h3 (RRM_hnRNPH_ESRPs_RBM12_like)

PHATRDRAFT_10024 - heterogeneous nuclear ribonucleoprotein h3 (RRM_hnRNPH_ESRPs_RBM12_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10024
PHATRDRAFT_11259 epc1 (ectopically parting cells)transferring glycosyl groups (Glyco_transf_64 superfamily)

PHATRDRAFT_11259 - epc1 (ectopically parting cells)transferring glycosyl groups (Glyco_transf_64 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11259
PHATRDRAFT_11826 sugar transporter family protein (SP)

PHATRDRAFT_11826 - sugar transporter family protein (SP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11826
PHATRDRAFT_14699 novel proteinvertebrate ring finger and chy zinc finger domain containing 1(zgc:101128) (zf-CHY superfamily)

PHATRDRAFT_14699 - novel proteinvertebrate ring finger and chy zinc finger domain containing 1(zgc:101128) (zf-CHY superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14699
PHATRDRAFT_14770 cytochrome c oxidase assembly factor (SCO)

PHATRDRAFT_14770 - cytochrome c oxidase assembly factor (SCO)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14770
PHATRDRAFT_18469 d-xylose proton-symporter (Sugar_tr)

PHATRDRAFT_18469 - d-xylose proton-symporter (Sugar_tr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18469
PHATRDRAFT_2808 protein disulfide isomerase associated 6 (Thioredoxin_like superfamily)

PHATRDRAFT_2808 - protein disulfide isomerase associated 6 (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2808
PHATRDRAFT_31684 soul heme-binding protein (DUF2358 superfamily)

PHATRDRAFT_31684 - soul heme-binding protein (DUF2358 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31684
PHATRDRAFT_32813 glutathione s-transferase-like protein

PHATRDRAFT_32813 - glutathione s-transferase-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32813
PHATRDRAFT_33005

PHATRDRAFT_33005 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33005
PHATRDRAFT_33590 major facilitator family transporter (2A0106)

PHATRDRAFT_33590 - major facilitator family transporter (2A0106)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33590
PHATRDRAFT_35054 agc family protein kinase (S_TKc)

PHATRDRAFT_35054 - agc family protein kinase (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35054
PHATRDRAFT_35296 loc100125051 protein (MATE_like superfamily)

PHATRDRAFT_35296 - loc100125051 protein (MATE_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35296
PHATRDRAFT_36109 (MMACHC-like)

PHATRDRAFT_36109 - (MMACHC-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36109
PHATRDRAFT_37648

PHATRDRAFT_37648 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37648
PHATRDRAFT_41069 (PAP_fibrillin superfamily)

PHATRDRAFT_41069 - (PAP_fibrillin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41069
PHATRDRAFT_43301 integral membrane protein (Ureide_permease superfamily)

PHATRDRAFT_43301 - integral membrane protein (Ureide_permease superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43301
PHATRDRAFT_45216 (PqiA superfamily)

PHATRDRAFT_45216 - (PqiA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45216
PHATRDRAFT_45504 dehydrogenase reductase 1 (NADB_Rossmann superfamily)

PHATRDRAFT_45504 - dehydrogenase reductase 1 (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45504
PHATRDRAFT_45579

PHATRDRAFT_45579 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45579
PHATRDRAFT_46017

PHATRDRAFT_46017 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46017
PHATRDRAFT_46136 phosphatidate cytidylyltransferase (ADP_ribosyl_GH)

PHATRDRAFT_46136 - phosphatidate cytidylyltransferase (ADP_ribosyl_GH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46136
PHATRDRAFT_46389 aspartyl protease family protein (pepsin_retropepsin_like superfamily)

PHATRDRAFT_46389 - aspartyl protease family protein (pepsin_retropepsin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46389
PHATRDRAFT_47564 endomembrane protein (EMP70 superfamily)

PHATRDRAFT_47564 - endomembrane protein (EMP70 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47564
PHATRDRAFT_48132

PHATRDRAFT_48132 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48132
PHATRDRAFT_48170 3-phosphoinositide-dependent protein kinase 1 (S_TKc)

PHATRDRAFT_48170 - 3-phosphoinositide-dependent protein kinase 1 (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48170
PHATRDRAFT_48257

PHATRDRAFT_48257 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48257
PHATRDRAFT_48575

PHATRDRAFT_48575 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48575
PHATRDRAFT_48599

PHATRDRAFT_48599 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48599
PHATRDRAFT_48882 light-harvesting chlorophyll a-c binding protein (Chloroa_b-bind superfamily)

PHATRDRAFT_48882 - light-harvesting chlorophyll a-c binding protein (Chloroa_b-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48882
PHATRDRAFT_49462 diacylglycerol (LPLAT_MGAT-like)

PHATRDRAFT_49462 - diacylglycerol (LPLAT_MGAT-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49462
PHATRDRAFT_8154 fk506 binding protein 7 (FKBP_C)

PHATRDRAFT_8154 - fk506 binding protein 7 (FKBP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8154
PHATRDRAFT_83 abc transporter (ABCG_PDR_domain2)

PHATRDRAFT_83 - abc transporter (ABCG_PDR_domain2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_83
GO ID Go Term p-value q-value Cluster
GO:0006508 proteolysis and peptidolysis 0.620715 1 Phatr_bicluster_0148
GO:0008152 metabolism 0.723107 1 Phatr_bicluster_0148
GO:0008643 carbohydrate transport 0.00192368 1 Phatr_bicluster_0148
GO:0006810 transport 0.00703653 1 Phatr_bicluster_0148
GO:0008654 phospholipid biosynthesis 0.0371948 1 Phatr_bicluster_0148
GO:0006979 response to oxidative stress 0.0963076 1 Phatr_bicluster_0148
GO:0009765 photosynthesis light harvesting 0.151992 1 Phatr_bicluster_0148
GO:0006468 protein amino acid phosphorylation 0.161086 1 Phatr_bicluster_0148
GO:0006118 electron transport 0.249468 1 Phatr_bicluster_0148
GO:0016567 protein ubiquitination 0.263338 1 Phatr_bicluster_0148
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