Organism : Methanococcus maripaludis S2 | Module List :
MMP0999

hypothetical protein MMP0999

CircVis
Functional Annotations (4)
Function System
Predicted membrane protein cog/ cog
proteolysis go/ biological_process
serine-type peptidase activity go/ molecular_function
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0999
(Mouseover regulator name to see its description)

MMP0999 is regulated by 8 influences and regulates 0 modules.
Regulators for MMP0999 (8)
Regulator Module Operator
MMP0217
MMP1303		 95 combiner
MMP1100
MMP1646		 95 combiner
MMP1376
MMP1646		 95 combiner
MMP0033
H2		 140 combiner
MMP0033
MMP0629		 140 combiner
MMP0052
MMP0257		 140 combiner
MMP0637 140 tf
MMP1467
MMP1646		 140 combiner

Warning: MMP0999 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
847 3.20e+01 GGCcaagGCc
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848 5.00e+01 CGaGGgAtaTg
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931 1.10e-02 aTCTGGTG
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932 1.10e+02 GGGTTCAAATCCCcccCacaGCGC
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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 MMP0999

MMP0999 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted membrane protein cog/ cog
proteolysis go/ biological_process
serine-type peptidase activity go/ molecular_function
membrane go/ cellular_component
Module neighborhood information for MMP0999

MMP0999 has total of 68 gene neighbors in modules 95, 140
Gene neighbors (68)
Gene Common Name Description Module membership
MMP0046 hypothetical protein MMP0046 20, 51, 140
MMP0074 hypothetical protein MMP0074 51, 140
MMP0104 polyferredoxin 95, 107
MMP0106 hypothetical protein MMP0106 107, 140
MMP0108 ABC-type Iron(III)-binding periplasmic protein precursor 41, 67, 95
MMP0133 guaB inosine-5'-monophosphate dehydrogenase 25, 120, 140
MMP0178 purQ phosphoribosylformylglycinamidine synthase I 95, 143
MMP0210 hypothetical protein MMP0210 58, 140
MMP0216 cation transport ATPase 4, 41, 95
MMP0220 Sodium/proline symporter-related 70, 140
MMP0224 hemL glutamate-1-semialdehyde aminotransferase 60, 130, 140
MMP0253 acd CoA-binding domain-containing protein 95, 124
MMP0271 putative ATP binding nickel incorporation protein 21, 95
MMP0282 purE phosphoribosylaminoimidazole carboxylase catalytic subunit 7, 140
MMP0319 cbiL precorrin-2 C-20 methyltransferase 24, 140, 141, 149
MMP0346 2-hydroxyglutaryl-CoA dehydratase subunit D-like protein 7, 140
MMP0354 putative oligosaccharide transporter 80, 95
MMP0356 group 1 glycosyl transferase 80, 139, 140
MMP0479 hypothetical protein MMP0479 4, 95
MMP0530 hypothetical protein MMP0530 92, 140
MMP0531 hypothetical protein MMP0531 106, 140
MMP0541 serB phosphoserine phosphatase SerB 7, 40, 139, 140
MMP0550 amino acid ABC transporter periplasmic protein 81, 140
MMP0554 SAM-binding motif-containing protein 129, 140
MMP0588 dph5 diphthine synthase 25, 81, 140
MMP0609 pth2 peptidyl-tRNA hydrolase 66, 140
MMP0705 wbpI UDP-N-acetylglucosamine 2-epimerase 80, 140
MMP0707 sodium/hydrogen exchanger 87, 109, 140
MMP0849 L-lysine/ homoserine-homoserine lactone exporter family protein 95, 117
MMP0861 kamA lysine 2,3-aminomutase 41, 95
MMP0862 yodP GCN5-like N-acetyltransferase 41, 95
MMP0865 aminotransferase (subgroup II) adenosylmethionine-8-amino-7-oxononanoate aminotransferase 115, 140
MMP0873 hypothetical protein MMP0873 95, 107
MMP0878 ribonuclease P-like protein 25, 87, 140
MMP0880 aksF isopropylmalate/isohomocitrate dehydrogenase 24, 60, 140, 143
MMP0999 hypothetical protein MMP0999 95, 140
MMP1000 hypothetical protein MMP1000 4, 95
MMP1068 K+-dependent Na+/Ca+ exchanger related-protein:Sodium/calcium exchanger membrane region 81, 140
MMP1099 phosphate transporter PhoU 66, 89, 95
MMP1106 hypothetical protein MMP1106 81, 137, 140
MMP1150 mtaA uroporphyrinogen decarboxylase 4, 41, 95
MMP1199 phosphate transporter PhoU 95, 133
MMP1210 hypothetical protein MMP1210 89, 95
MMP1212 acetyl-CoA acetyltransferase 89, 95
MMP1219 putative dinG ATP-dependent helicase 95, 107
MMP1232 PP-loop domain-containing protein 95, 104
MMP1312 hypothetical protein MMP1312 52, 140
MMP1326 rpoN DNA-directed RNA polymerase subunit N 103, 118, 140
MMP1337 hydrogenase maturation protease 95, 107
MMP1353 hypothetical protein MMP1353 81, 140
MMP1356 PP-loop domain-containing protein 25, 129, 139, 140, 149
MMP1357 hypothetical protein MMP1357 140, 149
MMP1362 rpoB1 DNA-directed RNA polymerase subunit B' 63, 130, 140
MMP1425 tRNA 2'-O-methylase 25, 87, 140
MMP1426 dcd bifunctional dCTP deaminase/dUTP diphosphatase 16, 112, 140
MMP1429 rpm DNA-directed RNA polymerase subunit M 95, 107
MMP1438 hypothetical protein MMP1438 14, 140
MMP1466 ehaS putative CBS domain-containing signal transduction protein 95, 107, 133
MMP1540 hypothetical protein MMP1540 24, 140
MMP1612 hypothetical protein MMP1612 41, 95
MMP1651 modA molybdenum ABC transporter periplasmic molybdate-binding protein 41, 95
MMP1652 molybdate ABC transporter periplasmic substrate-binding protein 89, 95
Unanno_12 None 89, 95
Unanno_24 None 95, 143
Unanno_28 None 41, 95
Unanno_49 None 95, 117
Unanno_5 None 95, 107
Unanno_60 None 95, 107
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 MMP0999
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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