Phatr_bicluster_0169 Residual: 0.42
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_0169 0.42 Phaeodactylum tricornutum
Displaying 1 - 38 of 38
PHATRDRAFT_11197 nuclear pore complex component (sc seh1) (DUF2499)

PHATRDRAFT_11197 - nuclear pore complex component (sc seh1) (DUF2499)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11197
PHATRDRAFT_11336 (Abhydrolase_6)

PHATRDRAFT_11336 - (Abhydrolase_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11336
PHATRDRAFT_11934 translation initiation factor if-1 (S1_IF1)

PHATRDRAFT_11934 - translation initiation factor if-1 (S1_IF1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11934
PHATRDRAFT_12375 pyruvate dehydrogenase e1 component alpha subunit (TPP_E1_PDC_ADC_BCADC)

PHATRDRAFT_12375 - pyruvate dehydrogenase e1 component alpha subunit (TPP_E1_PDC_ADC_BCADC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12375
PHATRDRAFT_12411 fkbp-type peptidyl-prolyl (FKBP_C)

PHATRDRAFT_12411 - fkbp-type peptidyl-prolyl (FKBP_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12411
PHATRDRAFT_14715 50s ribosomal protein l10 (Ribosomal_L10)

PHATRDRAFT_14715 - 50s ribosomal protein l10 (Ribosomal_L10)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14715
PHATRDRAFT_31407 at3g61320 t20k12_220 (Bestrophin superfamily)

PHATRDRAFT_26635 - at3g61320 t20k12_220 (Bestrophin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26635
PHATRDRAFT_32559 l-aspartate oxidase (NadB)

PHATRDRAFT_30807 - l-aspartate oxidase (NadB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30807
PHATRDRAFT_33907 cyclase dehydrase-like protein (SRPBCC superfamily)

PHATRDRAFT_31407 - cyclase dehydrase-like protein (SRPBCC superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31407
PHATRDRAFT_34382 abc transporter-like protein (ABC_ATPase superfamily)

PHATRDRAFT_32559 - abc transporter-like protein (ABC_ATPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32559
PHATRDRAFT_34592

PHATRDRAFT_33907 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33907
PHATRDRAFT_35949

PHATRDRAFT_34382 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34382
PHATRDRAFT_36034 cry dash-like protein (crypto_DASH)

PHATRDRAFT_34592 - cry dash-like protein (crypto_DASH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34592
PHATRDRAFT_42845 mitochondrial carrier protein (Mito_carr)

PHATRDRAFT_35949 - mitochondrial carrier protein (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35949
PHATRDRAFT_43223 yggt family protein (YGGT)

PHATRDRAFT_36034 - yggt family protein (YGGT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36034
PHATRDRAFT_43374

PHATRDRAFT_42845 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42845
PHATRDRAFT_44400 quiescin q6-like 1 (Thioredoxin_like superfamily)

PHATRDRAFT_43223 - quiescin q6-like 1 (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43223
PHATRDRAFT_44401 retinal pigment epithelial membrane protein (RPE65 superfamily)

PHATRDRAFT_43374 - retinal pigment epithelial membrane protein (RPE65 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43374
PHATRDRAFT_44450

PHATRDRAFT_44400 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44400
PHATRDRAFT_44796 (NADB_Rossmann superfamily)

PHATRDRAFT_44401 - (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44401
PHATRDRAFT_44831

PHATRDRAFT_44450 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44450
PHATRDRAFT_44892 (FUN14)

PHATRDRAFT_44796 - (FUN14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44796
PHATRDRAFT_44899 protein tyrosine (PTPLA)

PHATRDRAFT_44831 - protein tyrosine (PTPLA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44831
PHATRDRAFT_45565 ribosomal protein l11 methyltransferase (LsmAD)

PHATRDRAFT_44892 - ribosomal protein l11 methyltransferase (LsmAD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44892
PHATRDRAFT_46064 membrane protein (DUF3464)

PHATRDRAFT_44899 - membrane protein (DUF3464)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44899
PHATRDRAFT_46172 cyclin delta-3

PHATRDRAFT_45565 - cyclin delta-3

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45565
PHATRDRAFT_47005

PHATRDRAFT_46064 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46064
PHATRDRAFT_47824 possible gram-negative pili assembly chaperone

PHATRDRAFT_46172 - possible gram-negative pili assembly chaperone

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46172
PHATRDRAFT_48080 prenylcysteine oxidase 1 (Prenylcys_lyase superfamily)

PHATRDRAFT_47005 - prenylcysteine oxidase 1 (Prenylcys_lyase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47005
PHATRDRAFT_48510 af323582_1beta transducin-like protein het-e2c (WD40 superfamily)

PHATRDRAFT_47824 - af323582_1beta transducin-like protein het-e2c (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47824
PHATRDRAFT_50387 pap 25a associated domain containingexpressed (NT_PAP_TUTase)

PHATRDRAFT_48080 - pap 25a associated domain containingexpressed (NT_PAP_TUTase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48080
PHATRDRAFT_51120 high-affinity nickel-transport family protein

PHATRDRAFT_48510 - high-affinity nickel-transport family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48510
PHATRDRAFT_5217 sjchgc04996 protein (GRASP55_65 superfamily)

PHATRDRAFT_50387 - sjchgc04996 protein (GRASP55_65 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50387
PHATRDRAFT_54134 leucyl-trna synthetase (leuS)

PHATRDRAFT_51120 - leucyl-trna synthetase (leuS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51120
PHATRDRAFT_7335 pseudouridylate synthase 3 (PseudoU_synth superfamily)

PHATRDRAFT_5217 - pseudouridylate synthase 3 (PseudoU_synth superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5217
PHATRDRAFT_8310 glutamyl-trna reductase (PLN00203)

PHATRDRAFT_54134 - glutamyl-trna reductase (PLN00203)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54134

PHATRDRAFT_7335 - peptide methionine sulfoxide reductase (PMSR superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7335

PHATRDRAFT_8310 - at1g64350 f15h21_2 (DUF3593 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8310
GO ID Go Term p-value q-value Cluster
GO:0006429 leucyl-tRNA aminoacylation 0.00296369 1 Phatr_bicluster_0169
GO:0042254 ribosome biogenesis and assembly 0.0176618 1 Phatr_bicluster_0169
GO:0008033 tRNA processing 0.0577662 1 Phatr_bicluster_0169
GO:0006413 translational initiation 0.0689457 1 Phatr_bicluster_0169
GO:0006281 DNA repair 0.0963646 1 Phatr_bicluster_0169
GO:0006418 tRNA aminoacylation for protein translation 0.143861 1 Phatr_bicluster_0169
GO:0006118 electron transport 0.144823 1 Phatr_bicluster_0169
GO:0006464 protein modification 0.171749 1 Phatr_bicluster_0169
GO:0006457 protein folding 0.296964 1 Phatr_bicluster_0169
GO:0006810 transport 0.440472 1 Phatr_bicluster_0169
Log in to post comments