Organism : Methanococcus maripaludis S2 | Module List :
MMP1106

hypothetical protein MMP1106

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1106
(Mouseover regulator name to see its description)

MMP1106 is regulated by 17 influences and regulates 0 modules.
Regulators for MMP1106 (17)
Regulator Module Operator
MMP0033
H2
140 combiner
MMP0033
MMP0629
140 combiner
MMP0052
MMP0257
140 combiner
MMP0637 140 tf
MMP1467
MMP1646
140 combiner
H2 81 ef
MMP0020 81 tf
MMP0020
MMP0752
81 combiner
MMP0020
MMP0791
81 combiner
MMP0052 81 tf
MMP0052
MMP0480
81 combiner
MMP0168
MMP1100
81 combiner
MMP0637 81 tf
MMP1015 81 tf
MMP1376 81 tf
MMP1467
MMP1646
81 combiner
H2 137 ef

Warning: MMP1106 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
823 6.40e-01 GGTGAttT
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824 1.90e+04 cggTTTTacgTaG
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925 2.30e+03 GTTCGATtg.g..TCT.g.ctC
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926 5.30e+03 AAACaAtGtTTtattaTacg
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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 MMP1106

Warning: No Functional annotations were found!

Module neighborhood information for MMP1106

MMP1106 has total of 68 gene neighbors in modules 81, 137, 140
Gene neighbors (68)
Gene Common Name Description Module membership
MMP0046 hypothetical protein MMP0046 20, 51, 140
MMP0074 hypothetical protein MMP0074 51, 140
MMP0106 hypothetical protein MMP0106 107, 140
MMP0133 guaB inosine-5'-monophosphate dehydrogenase 25, 120, 140
MMP0145 hpt adenine phosphoribosyltransferase 137, 143
MMP0146 hypothetical protein MMP0146 17, 41, 137
MMP0187 thiC thiamine biosynthesis protein ThiC 137, 143
MMP0210 hypothetical protein MMP0210 58, 140
MMP0212 glycyl-tRNA synthetase 81, 107
MMP0220 Sodium/proline symporter-related 70, 140
MMP0224 hemL glutamate-1-semialdehyde aminotransferase 60, 130, 140
MMP0282 purE phosphoribosylaminoimidazole carboxylase catalytic subunit 7, 140
MMP0297 aIF-2_beta translation initiation factor IF-2 subunit beta 60, 81
MMP0319 cbiL precorrin-2 C-20 methyltransferase 24, 140, 141, 149
MMP0346 2-hydroxyglutaryl-CoA dehydratase subunit D-like protein 7, 140
MMP0356 group 1 glycosyl transferase 80, 139, 140
MMP0404 cofD 2-phospho-L-lactate transferase 87, 137
MMP0414 thrS threonyl-tRNA synthetase 8, 81, 112
MMP0417 hisA 1-(5-phosphoribosyl)-5- 60, 137
MMP0418 carbohydrate kinase PfkB 60, 137, 143
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
MMP0596 C/D box methylation guide ribonucleoprotein complex aNOP56 subunit 20, 81
MMP0597 flpA fibrillarin 8, 16, 81
MMP0606 ribosomal RNA methyltransferase RrmJ/FtsJ 137, 143
MMP0607 nrpR hypothetical protein MMP0607 115, 137, 143
MMP0609 pth2 peptidyl-tRNA hydrolase 66, 140
MMP0705 wbpI UDP-N-acetylglucosamine 2-epimerase 80, 140
MMP0707 sodium/hydrogen exchanger 87, 109, 140
MMP0865 aminotransferase (subgroup II) adenosylmethionine-8-amino-7-oxononanoate aminotransferase 115, 140
MMP0878 ribonuclease P-like protein 25, 87, 140
MMP0880 aksF isopropylmalate/isohomocitrate dehydrogenase 24, 60, 140, 143
MMP0881 hypothetical protein MMP0881 111, 137
MMP0899 ATP/GTP-binding motif-containing protein 70, 81
MMP0900 rhodanese domain-containing protein 70, 81
MMP0946 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B 8, 81, 96
MMP0999 hypothetical protein MMP0999 95, 140
MMP1063 leuA 2-isopropylmalate synthase 81, 143
MMP1068 K+-dependent Na+/Ca+ exchanger related-protein:Sodium/calcium exchanger membrane region 81, 140
MMP1081 wbpG putative LPS biosynthesis protein WbpG 137, 143
MMP1083 imidazole glycerol phosphate synthase subunit HisF 137, 143
MMP1105 sucC succinate-CoA ligase (ADP-forming), beta chain 7, 81, 137
MMP1106 hypothetical protein MMP1106 81, 137, 140
MMP1122 translation-associated GTPase 137, 143
MMP1131 peptide chain release factor 1 20, 81
MMP1146 purF amidophosphoribosyltransferase 7, 60, 137, 143
MMP1206 glnA glutamine synthetase 99, 137
MMP1242 nadA quinolinate synthetase 27, 81
MMP1312 hypothetical protein MMP1312 52, 140
MMP1316 korB 2-oxoglutarate ferredoxin oxidoreductase subunit beta 7, 120, 137
MMP1326 rpoN DNA-directed RNA polymerase subunit N 103, 118, 140
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
MMP1427 hypothetical protein MMP1427 81, 112
MMP1438 hypothetical protein MMP1438 14, 140
MMP1440 tRNA-modifying protein 129, 137
MMP1496 pheS phenylalanyl-tRNA synthetase subunit alpha 137, 143
MMP1532 pgk phosphoglycerate kinase 120, 137
MMP1540 hypothetical protein MMP1540 24, 140
MMP1656 glutamine amidotransferase subunit PdxT 8, 137
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 MMP1106
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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