Proteomic Signature Library for
Staphylococcus aureus COL

quick links

 

please cite

If Aureolib enriched your work we would like to ask to cite us:

Aureolib - a proteome signature library: towards an understanding of Staphylococcus aureus pathophysiology.
Fuchs S, Zühlke D, Pané-Farré J, Kusch H, Wolf C, Reiß S, Binh le TN, Albrecht D, Riedel K, Hecker M, Engelmann S.
PLoS One. 2013 Aug 13;8(8):e70669. doi: 10.1371/journal.pone.0070669. eCollection 2013.

Free full text
 

experiments

Data of following signatures are available in the library (see references for experimental details):
 
:: experiment description imported reference
1 hydrogen peroxide stress of exponentially grown cells (CDM; OD 0.5; 37°C) by H2O2 [10 mM] 2012-05-18 Wolf et al., 2008
2 diamide stress of exponentially grown cells (CDM; OD 0.5; 37°C) by diamide [1 mM] 2012-05-18 Wolf et al., 2008
3 paraquat stress of exponentially grown cells (CDM; OD 0.5; 37°C) by paraquat [0.01 µM] 2012-05-18 Wolf et al., 2008
4 nitric oxide stress of exponentially grown cells (CDM; OD 0.5; 37°C) by NO [500 µM] 2012-05-18 Hochgräfe et al., 2008
5 fermentation shift of exponentially grown cells (CDM; OD 0.5; 37°C) to oxygen limitation 2012-05-18 Fuchs et al., 2007
6 nitrate respiration shift of exponentially grown cells (CDM + NO3 [8mM]; OD 0.5; 37°C) to oxygen limitation 2012-05-18 Fuchs et al., 2007
7 heat shift of exponentially grown cells (CDM; OD 0.5; 37°C) to 48°C 2015-07-15 Fuchs et al., 2013
8 puromycin stress of exponentially grown cells (CDM; OD 0.5; 37°C) by puromycin [3 µM] 2015-07-15 Fuchs et al., 2013
9 mupirocin stress of exponentially grown cells (CDM; OD 0.5; 37°C) by mupirocin [0.03 µg/ml] 2012-05-18 Reiß et al., 2012
 

sampling

Timepoints and number of independent biological replicates used for the 35S-methionine labeling:
 
:: experiment controls samples
0'60' 1'5'10'20'30'40'60'120'
1 hydrogen peroxide 2--22-222-
2 diamide 2--22-222-
3 paraquat 2--22-2-22
4 nitric oxide 2-222-2-2-
5 fermentation 22--222-2-
6 nitrate respiration 22--222-2-
7 heat 3--33-2-3-
8 puromycin 33-33-3-3-
9 mupirocin 22--2-2-2-
 

transfer of identification labels

A reference map (mastergel) containing the identification data as so-called labels were created. These labels were manually transferred to each experiment. Only labels transferred without any doubt and within experiment-specifically detected spot borders are considered.
 
:: experiment considered labels considered protein spots
1 hydrogen peroxide 542 490
2 diamide 579 539
3 paraquat 566 511
4 nitric oxide 547 503
5 fermentation 598 542
6 nitrate respiration 548 503
7 heat 516 496
8 puromycin 576 543
9 mupirocin 593 565
 

statistical analyses

For statistical analysis ANOVA (1st level, end controls excluded) and t-test (2nd level, single timepoints vs control at t0) were perfomed applying the following parameters (see references for details of analysis):
 
:: experiment ANOVA t-TEST reference
1 hydrogen peroxide α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
2 diamide α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
3 paraquat α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
4 nitric oxide α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
5 fermentation α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
6 nitrate respiration α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
7 heat α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
8 puromycin α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
9 mupirocin α=0.1, distribution based on 1000 permutations α=0.1, distribution based on 1000 permutations, adjusted Bonferroni correction Fuchs et al., in prep.
 

regulons & regulatory elements

Considered regulons and regulatoric elements:
 
:: regulator/
regulatory element
assigned proteins for which expression data is available assigned proteins for which expression data is NOT available
1 AgrA 0 5
2 ArcR 0 5
3 ArgR 2 14
4 ArsR 0 3
5 BglR 0 3
6 BirA 0 12
7 BlaI 0 0
8 CcpA 18 102
9 CodY 49 97
10 CtsR 8 4
11 CymR 4 15
12 CzrA 0 2
13 FapR 6 2
14 FMN 2 3
15 FruR 0 2
16 Fur 3 46
17 GapR 6 0
18 GlmS 1 0
19 GlnR 1 2
20 GltC 1 2
21 GlvR 0 1
22 Glycine 1 2
23 GntR 0 3
24 HisR 0 13
25 HrcA 5 1
26 HssR 0 2
27 HutR 0 4
28 IcaR 0 4
29 L10_leader 2 0
30 L13_leader 0 2
31 L19_leader 0 1
32 L20_leader 0 3
33 LacR 0 7
34 LexA 6 10
35 Lysine 7 2
36 MalR 0 9
37 ManR 0 2
38 MecI 0 2
39 MepR 0 2
40 MntR 0 4
41 MtlR 2 2
42 MurR 0 4
43 NrdR 2 3
44 NreC 0 12
45 PdxR 1 1
46 PerR 15 2
47 PreQ1 0 4
48 Purine 3 1
49 PurR 12 2
50 PyrR 6 2
51 RbsR 0 3
52 SaeR 1 25
53 SAM 2 4
54 ScrR 2 1
55 T-box(Ala) 1 0
56 T-box(Asn) 1 1
57 T-box(Cys) 1 1
58 T-box(Gly) 1 0
59 T-box(Ile) 1 0
60 T-box(Leu) 1 0
61 T-box(Met) 5 0
62 T-box(Phe) 2 0
63 T-box(Ser) 1 0
64 T-box(Thr) 1 0
65 T-box(Trp) 0 7
66 T-box(Tyr) 1 0
67 T-box(Val) 1 0
68 TPP 0 7
69 TreR 0 3
70 YtrA 0 5
71 yybP-ykoY 0 1
72 Zur 1 11
73 SigB- 4 62
74 SigB+ 40 186
75 Rex 8 18
 

the online system

The online system is currently running under: Valid CSS 2Valid HTML 4.01 Transitional
PHP (5.6.38)
MySQL (5.6.41)
 
For full functionality JAVAScript has to be enabled and the free Flash plugin is needed.
 
Data content includes:
9 signatures
94 autoradiograms
698 expression profiles
 
The changelog can be found here.
 

funds

Universität Greifswald TRR 34
 

impressum & contact

Information provided according to Sec. 5 German Telemedia Act (TMG):

idea, concept, design, programming, domain holder:

Stephan Fuchs
Westernstr. 5
38855 Wernigerode

Contact:

Telephone: +4932224143575
Telefax: +4932224143575
Email: info@aureolib.de

 

disclaimer

Liability for Contents

As service providers, we are liable for own contents of these websites according to Sec. 7, paragraph 1 German Telemedia Act (TMG). However, according to Sec. 8 to 10 German Telemedia Act (TMG), service providers are not obligated to permanently monitor submitted or stored information or to search for evidences that indicate illegal activities.

Legal obligations to removing information or to blocking the use of information remain unchallenged. In this case, liability is only possible at the time of knowledge about a specific violation of law. Illegal contents will be removed immediately at the time we get knowledge of them.

Liability for Links

Our offer includes links to external third party websites. We have no influence on the contents of those websites, therefore we cannot guarantee for those contents. Providers or administrators of linked websites are always responsible for their own contents.

The linked websites had been checked for possible violations of law at the time of the establishment of the link. Illegal contents were not detected at the time of the linking. A permanent monitoring of the contents of linked websites cannot be imposed without reasonable indications that there has been a violation of law. Illegal links will be removed immediately at the time we get knowledge of them.

Copyright

Contents and compilations published on these websites by the providers are subject to German copyright laws. Reproduction, editing, distribution as well as the use of any kind outside the scope of the copyright law require a written permission of the author or originator. Downloads and copies of these websites are permitted for private use only.
The commercial use of our contents without permission of the originator is prohibited.

Copyright laws of third parties are respected as long as the contents on these websites do not originate from the provider. Contributions of third parties on this site are indicated as such. However, if you notice any violations of copyright law, please inform us. Such contents will be removed immediately.

 

privacy policy

1. An overview of data protection

General

The following gives a simple overview of what happens to your personal information when you visit our website. Personal information is any data with which you could be personally identified. Detailed information on the subject of data protection can be found in our privacy policy found below.

Data collection on our website

Who is responsible for the data collection on this website?

The data collected on this website are processed by the website operator. The operator's contact details can be found in the website's impressum.

How do we collect your data?

Some data are collected when you provide it to us. This are, for example, data you enter to search expressiopn profiles or define plot settings. Such data is stored to provide but not linked to any perosnal information such as your IP address.

Other data are collected automatically by our IT systems when you visit the website. These data are primarily technical data such as the browser and operating system you are using or when you accessed the page. These data are collected automatically as soon as you enter our website.

What do we use your data for?

Part of the data is collected to ensure the proper functioning of the website. Other data can be used to analyze how visitors use the site.

Analytics and third-party tools

When visiting our website, statistical analyses may be made of your surfing behavior. This happens primarily using cookies and analytics. The analysis of your surfing behavior is usually anonymous, i.e. we will not be able to identify you from this data. You can object to this analysis or prevent it by not using certain tools. Detailed information can be found in the following privacy policy.

You can object to this analysis. We will inform you below about how to exercise your options in this regard.

2. General information and mandatory information

Data protection

The operators of this website take the protection of your personal data very seriously. We treat your personal data as confidential and in accordance with the statutory data protection regulations and this privacy policy.

If you use this website, various pieces of personal data will be collected. Personal information is any data with which you could be personally identified. This privacy policy explains what information we collect and what we use it for. It also explains how and for what purpose this happens.

Please note that data transmitted via the internet (e.g. via email communication) may be subject to security breaches. Complete protection of your data from third-party access is not possible.

Notice concerning the party responsible for this website

The party responsible for processing data on this website is:

Stephan Fuchs
Westernstr. 5
3885 Wernigerode
Germany

Telephone: +4932224143575
Email: info@aureolib.de

The responsible party is the natural or legal person who alone or jointly with others decides on the purposes and means of processing personal data (names, email addresses, etc.).

Right to file complaints with regulatory authorities

If there has been a breach of data protection legislation, the person affected may file a complaint with the competent regulatory authorities. The competent regulatory authority for matters related to data protection legislation is the data protection officer of the German state in which the site owner is living (see impressum). A list of data protection officers and their contact details can be found at the following link: https://www.bfdi.bund.de/DE/Infothek/Anschriften_Links/anschriften_links-node.html.

Opposition to promotional emails

We hereby expressly prohibit the use of contact data published in the context of website legal notice requirements with regard to sending promotional and informational materials not expressly requested. The website operator reserves the right to take specific legal action if unsolicited advertising material, such as email spam, is received.

3. Data collection on our website

Cookies

Some of our web pages use cookies. Cookies do not harm your computer and do not contain any viruses. Cookies help make our website more user-friendly, efficient, and secure. Cookies are small text files that are stored on your computer and saved by your browser.

Most of the cookies we use are so-called "session cookies." They are automatically deleted after your visit. Other cookies remain in your device's memory until you delete them. These cookies make it possible to recognize your browser when you next visit the site.

You can configure your browser to inform you about the use of cookies so that you can decide on a case-by-case basis whether to accept or reject a cookie. Alternatively, your browser can be configured to automatically accept cookies under certain conditions or to always reject them, or to automatically delete cookies when closing your browser. Disabling cookies may limit the functionality of this website.

Cookies which are necessary to allow electronic communications or to provide certain functions you wish to use (such as the shopping cart) are stored pursuant to Art. 6 paragraph 1, letter f of DSGVO. The website operator has a legitimate interest in the storage of cookies to ensure an optimized service provided free of technical errors. If other cookies (such as those used to analyze your surfing behavior) are also stored, they will be treated separately in this privacy policy.

Server log files

The website provider automatically collects and stores information that your browser automatically transmits to us in "server log files". These are:

  • visited domain: We record for which domain log data is stored.
  • Anonymized client IP: We collect IP addresses to identify where our servers may be attacked from. Our server provider stores these for a maximum of seven days, as is customary in the industry. After this period, all IP adresses will be made anonymous. From the very beginning, the IP can only be viewed in anonymous form by the site owner. An example of anonymization: 123,456,789,001 becomes anon-123-456-165-41.invalid.
  • Timestamp: This is an indication of the day and time on which the website was accessed.
  • Request line: This is the path of the destination address without the domain. When a visitor clicks on an image of our website, the URL "domain.de/bild.jpg" is behind it. The request line is then "/bild.jpg".
  • Status code: Surely you've seen a 404-page. This is always displayed if a called page or file cannot be found. 404 is the status code that indicates that the visitor wanted to visit a non-existent page. The Internet Assigned Numbers Authority has defined a number of other status codes that are useful for error analysis: 200 means OK, for example - here the user was able to access the page without errors.
  • Size of the response body: When the visitor enters the website, he temporarily downloads data. These are, for example, the images and texts that he sees in his browser. The log file specifies how large this data is.
  • Referer sent from the client: The referer indicates from which page the visitor came to the website.
  • User agent sent by the client: For example, information about the type and version of the browser and the operating system used by the visitor.

These data will not be combined with data from other sources.

The basis for data processing is Art. 6 (1) (f) DSGVO, which allows the processing of data to fulfill a contract or for measures preliminary to a contract.

4. Analytics and advertising

Matomo (formerly Piwik)

This website uses the open source web analytics service Matomo. Matomo uses so-called "cookies". These are text files that are stored on your computer and that allow an analysis of the use of the website by you. For this purpose, the information generated by the cookie about the use of this website is stored on our server. The IP address is anonymized before it is stored.

Matomo cookies remain on your device until you delete them.

The storage of Matomo cookies is based on Art. 6 (1) (f) DSGVO. The website operator has a legitimate interest in analyzing user behavior in order to optimize both its website and its advertising.

The information generated by the cookies about your use of this website will not be disclosed to third parties. You can prevent these cookies being stored by selecting the appropriate settings in your browser. However, we wish to point out that doing so may mean you will not be able to enjoy the full functionality of this website.

If you do not agree with the storage and use of your data, you can disable this feature here. In this case, an opt-out cookie will be stored in your browser to prevent Matomo from storing your usage data. If you delete your cookies, this will mean that the opt-out cookie will also be deleted. You will then need to reactivate it when you return to our site if you wish your activity not to be tracked.