Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3650

Periplasmic serine proteases (ClpP class) (NCBI)

CircVis
Functional Annotations (3)
Function System
Periplasmic serine proteases (ClpP class) cog/ cog
proteolysis go/ biological_process
peptidase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3650
(Mouseover regulator name to see its description)

RSP_3650 is regulated by 33 influences and regulates 0 modules.
Regulators for RSP_3650 (33)
Regulator Module Operator
RSP_0607 196 tf
RSP_1014 196 tf
RSP_1077 196 tf
RSP_1220 196 tf
RSP_1776 196 tf
RSP_1790 196 tf
RSP_1871 196 tf
RSP_1925 196 tf
RSP_2079 196 tf
RSP_2201 196 tf
RSP_2494 196 tf
RSP_2533 196 tf
RSP_2780 196 tf
RSP_2963 196 tf
RSP_3317 196 tf
RSP_3322 196 tf
RSP_3448 196 tf
RSP_3528 196 tf
RSP_0068 68 tf
RSP_0402 68 tf
RSP_0607 68 tf
RSP_0641 68 tf
RSP_0760 68 tf
RSP_1092 68 tf
RSP_1785 68 tf
RSP_2130 68 tf
RSP_2182 68 tf
RSP_2610 68 tf
RSP_3024 68 tf
RSP_3094 68 tf
RSP_3341 68 tf
RSP_3667 68 tf
RSP_3731 68 tf

Warning: RSP_3650 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
7856 7.40e+03 ATTCACGAAGCGCGAAT
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7857 1.80e+04 TTTtCcGCAA
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8112 1.80e+03 aaA.acgaCgAgAt
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8113 6.90e+02 GgaGGATc
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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_3650

RSP_3650 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Periplasmic serine proteases (ClpP class) cog/ cog
proteolysis go/ biological_process
peptidase activity go/ molecular_function
Module neighborhood information for RSP_3650

RSP_3650 has total of 49 gene neighbors in modules 68, 196
Gene neighbors (49)
Gene Common Name Description Module membership
RSP_0013 RSP_0013 hypothetical protein (NCBI) 68, 91
RSP_0133 RSP_0133 Na+/H+ antiporter, NhaC family (NCBI) 73, 196
RSP_0139 RSP_0139 Ribosomal protein S6 (NCBI) 83, 196
RSP_0220 RSP_0220 hypothetical protein (NCBI) 68, 327
RSP_0301 RSP_0301 ABC branched chain amino acid transporter, substrate binding protein (NCBI) 68, 300
RSP_0326 RSP_0326 hypothetical protein (NCBI) 68, 188
RSP_0571 RSP_0571 tRNA pseudouridine synthase (NCBI) 68, 108
RSP_0684 RSP_0684 Possible oxidoreductase; Short-chain dehydrogenase/reductase SDR (NCBI) 196, 209
RSP_0748 RSP_0748 N-6 Adenine-specific DNA methylase (NCBI) 68, 288
RSP_0828 RSP_0828 Major facilitator superfamily (MFS) transporter (NCBI) 124, 196
RSP_1010 RSP_1010 possible esterase/lipase/thioesterase (NCBI) 196, 236
RSP_1013 RSP_1013 possible Hemolysin (NCBI) 68, 267
RSP_1116 RSP_1116 glycosyltransferase (NCBI) 196, 246
RSP_1119 RSP_1119 ABC protein exporter, fused ATPase and inner membrane subunits (NCBI) 196, 246
RSP_1137 RSP_1137 Histone deacetylase family protein (NCBI) 68, 108
RSP_1198 RSP_1198 hypothetical protein (NCBI) 196, 308
RSP_1203 RSP_1203 ABC multidrug efflux pump, fused ATPase and inner membrane subunits (NCBI) 196, 209
RSP_1215 ilvE putative IlvE, Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase (NCBI) 68, 381
RSP_1224 hemN putative Coproporphyrinogen III oxidase and related Fe-S oxidoreductases (NCBI) 68, 187
RSP_1423 RSP_1423 ParA family ATPase (NCBI) 68, 293
RSP_1425 RSP_1425 Plasmid replication initiation protein (NCBI) 42, 68
RSP_1443 RSP_1443 ABC sugar transporter, inner membrane subunit (NCBI) 68, 89
RSP_1445 RSP_1445 ABC sugar transporter, ATPase subunit (NCBI) 68, 89
RSP_1530 RSP_1530 hypothetical protein (NCBI) 137, 196
RSP_1577 putR Proline dehydrogenase transcriptional activator (NCBI) 68, 112
RSP_1752 RSP_1752 Putative creatinase (NCBI) 68, 346
RSP_1778 RSP_1778 TPR domain protein (NCBI) 68, 285
RSP_1779 ispE Putative 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (NCBI) 68, 285
RSP_1802 ccmB ABC heme exporter, inner membrane subunit CcmB (NCBI) 196, 299
RSP_2220 RSP_2220 possible flagellar motor switch protein (fliG) (NCBI) 73, 196
RSP_2316 dadA D-amino acid dehydrogenase (NCBI) 68, 375
RSP_2339 RSP_2339 hypothetical protein (NCBI) 28, 68
RSP_2348 RSP_2348 hypothetical protein (NCBI) 68, 293
RSP_2396 RSP_2396 hypothetical protein (NCBI) 196, 285
RSP_2732 RSP_2732 Major facilitator superfamily (MFS) transporter (NCBI) 68, 292
RSP_2742 RSP_2742 hypothetical protein (NCBI) 128, 196
RSP_3009 RSP_3009 None 183, 196
RSP_3024 RSP_3024 transcriptional regulator, IclR family/MhpR (NCBI) 68, 73
RSP_3027 rdxA RdxA, iron-sulfur cluster-binding protein (NCBI) 62, 196
RSP_3126 RSP_3126 Arsenite efflux pump, ACR3 family (NCBI) 54, 196
RSP_3190 RSP_3190 2Fe-2S ferredoxin (NCBI) 68, 244
RSP_3414 RSP_3414 ABC Fe+3-siderophore transporter, inner membrane subunit (NCBI) 74, 196
RSP_3579 RSP_3579 Heat shock protein Hsp20 (NCBI) 196, 253
RSP_3581 RSP_3581 hypothetical protein (NCBI) 196, 253
RSP_3649 RSP_3649 None 196, 241
RSP_3650 RSP_3650 Periplasmic serine proteases (ClpP class) (NCBI) 68, 196
RSP_3657 RSP_3657 putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase (NCBI) 196, 238
RSP_3790 RSP_3790 hypothetical protein (NCBI) 42, 68
RSP_3837 RSP_3837 hypothetical protein (NCBI) 38, 196
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_3650
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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