Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3435

possible DNA-binding protein (NCBI)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3435
(Mouseover regulator name to see its description)

RSP_3435 is regulated by 23 influences and regulates 0 modules.
Regulators for RSP_3435 (23)
Regulator Module Operator
RSP_0087 316 tf
RSP_0623 316 tf
RSP_1139 316 tf
RSP_1220 316 tf
RSP_1518 316 tf
RSP_2324 316 tf
RSP_2610 316 tf
RSP_3238 316 tf
RSP_3317 316 tf
RSP_0068 91 tf
RSP_0386 91 tf
RSP_0394 91 tf
RSP_0611 91 tf
RSP_0774 91 tf
RSP_1034 91 tf
RSP_1243 91 tf
RSP_1286 91 tf
RSP_2324 91 tf
RSP_2533 91 tf
RSP_2572 91 tf
RSP_2888 91 tf
RSP_2963 91 tf
RSP_3528 91 tf

Warning: RSP_3435 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
7902 6.60e+02 tcccGCccgcgcGcT
Loader icon
7903 2.10e+03 ATCCGcGCCgatGtGcAATG
Loader icon
8344 6.30e-03 AtAATATT
Loader icon
8345 6.00e-01 aagCCagAACAAgtAgCacAG
Loader icon
Motif Help

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.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for RSP_3435

Warning: No Functional annotations were found!

Module neighborhood information for RSP_3435

RSP_3435 has total of 48 gene neighbors in modules 91, 316
Gene neighbors (48)
Gene Common Name Description Module membership
RSP_0010 RSP_0010 homoserine O-succinyltransferase (NCBI) 91, 133
RSP_0011 RSP_0011 Predicted hydrolases or acyltransferases (alpha/beta hydrolase) (NCBI) 91, 366
RSP_0013 RSP_0013 hypothetical protein (NCBI) 68, 91
RSP_0014 RSP_0014 transcriptional regulator, TetR family (NCBI) 91, 215
RSP_0425 metG Methionyl-tRNA synthetase (NCBI) 311, 316
RSP_0478 RSP_0478 putative lysyl-tRNA synthetase (NCBI) 183, 316
RSP_0567 RSP_0567 Probable Methylated-DNA-(protein)-cysteine S-methyltransferase (NCBI) 316, 337
RSP_0774 RSP_0774 RNA binding protein (NCBI) 91, 184
RSP_0819 rhlE2 DEAD/DEAH box helicase (NCBI) 209, 316
RSP_1018 RSP_1018 Glycolate oxidase iron-sulfur subunit (NCBI) 91, 148
RSP_1019 RSP_1019 putative glycolate oxidase subunit protein (NCBI) 91, 148
RSP_1034 pdhR Pyruvate dehydrogenase complex repressor (NCBI) 91, 148
RSP_1128 dapE succinyl-diaminopimelate desuccinylase (NCBI) 69, 316
RSP_1130 RSP_1130 hypothetical membrane protein (NCBI) 54, 91
RSP_1172 dnaJ Chaperone, DnaJ (NCBI) 91, 297
RSP_1292 RSP_1292 putative Aldehyde dehydrogenase (NCBI) 91, 107
RSP_1426 RSP_1426 RNA-binding region RNP-1 (NCBI) 209, 316
RSP_1427 RSP_1427 hypothetical protein (NCBI) 209, 316
RSP_1487 RSP_1487 hypothetical protein (NCBI) 91, 289
RSP_1488 RSP_1488 Possible glyoxalase (NCBI) 91, 289
RSP_1516 RSP_1516 putative S-adenosyl L-homocystein hydrolase (NCBI) 91, 197
RSP_1895 RSP_1895 Small-conductance mechanosensitive ion channel (NCBI) 91, 231
RSP_1899 RSP_1899 Predicted ATPase (NCBI) 91, 220
RSP_1900 RSP_1900 hypothetical protein (NCBI) 91, 233
RSP_1901 RSP_1901 Hypothetical protein with TPR repeat (NCBI) 91, 245
RSP_2254 RSP_2254 ABC efflux transporter, fused ATPase and inner membrane subunits (NCBI) 115, 316
RSP_2263 RSP_2263 hypothetical protein (NCBI) 91, 125
RSP_2409 rluD putative Pseudouridine synthase, Rlu (NCBI) 54, 316
RSP_2456 radA DNA Repair Protein (NCBI) 39, 91
RSP_2552 exoU Glycosyl transferase, family 2 (NCBI) 209, 316
RSP_2558 RSP_2558 hypothetical protein (NCBI) 157, 316
RSP_2605 RSP_2605 hypothetical protein (NCBI) 91, 197
RSP_2606 RSP_2606 ArsR family Arsenical Resistance Operon Repressor (NCBI) 91, 197
RSP_2607 RSP_2607 nitrilotriacetate monooxygenase component B (NCBI) 91, 197
RSP_2608 corA magnesium/cobalt transport protein, MIT family (NCBI) 91, 197
RSP_2659 dgt Deoxyguanosinetriphosphate triphosphohydrolase (NCBI) 117, 316
RSP_2810 RSP_2810 ABC transporter, ATPase subunit (NCBI) 91, 294
RSP_3005 RSP_3005 hypothetical protein (NCBI) 40, 316
RSP_3006 RSP_3006 conserved hypothetical protein containing Von Willebrand factor, type A domain (NCBI) 40, 316
RSP_3107 RSP_3107 hypothetical protein (NCBI) 91, 350
RSP_3317 RSP_3317 transcriptional regulator, TetR family (NCBI) 247, 316
RSP_3318 acrB Cation/multidrug efflux pump, RND family (NCBI) 301, 316
RSP_3321 acrA Cation/multidrug efflux pump, membrane-fusion protein (NCBI) 301, 316
RSP_3384 RSP_3384 mandelate racemase/muconate lactonizing enzyme family protein (NCBI) 91, 346
RSP_3435 RSP_3435 possible DNA-binding protein (NCBI) 91, 316
RSP_3456 RSP_3456 Putative dihydrodipicolinate synthase (NCBI) 61, 91
RSP_3658 hpcH putative 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (NCBI) 105, 316
RSP_3785 RSP_3785 putative bacteriophage-related protein (NCBI) 91, 105
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for RSP_3435
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend