Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 1892 in total

Network Comparison Type	Subtracted
Interaction Map	High confidence
Filtered	1
red	0
green	0
network_comparison	0

Rank	description	Value Type	
2756	3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	Measured	
2756	3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	Ranked	
2756	3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	Squared	
2756	3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	Rooted	
2757	nucleosome assembly protein 1-like 1 (nap-1 related protein). [source:swissprot;acc:p55209]	Measured	
2757	nucleosome assembly protein 1-like 1 (nap-1 related protein). [source:swissprot;acc:p55209]	Ranked	
2757	nucleosome assembly protein 1-like 1 (nap-1 related protein). [source:swissprot;acc:p55209]	Squared	
2757	nucleosome assembly protein 1-like 1 (nap-1 related protein). [source:swissprot;acc:p55209]	Rooted	
2758	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [source:swissprot;acc:q9ulw6]	Measured	
2758	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [source:swissprot;acc:q9ulw6]	Ranked	
2758	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [source:swissprot;acc:q9ulw6]	Squared	
2758	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [source:swissprot;acc:q9ulw6]	Rooted	
2759	retinoic acid receptor rxr-alpha. [source:swissprot;acc:p19793]	Measured	
2759	retinoic acid receptor rxr-alpha. [source:swissprot;acc:p19793]	Ranked	
2759	retinoic acid receptor rxr-alpha. [source:swissprot;acc:p19793]	Squared	
2759	retinoic acid receptor rxr-alpha. [source:swissprot;acc:p19793]	Rooted	
2760	t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [source:swissprot;acc:q16559]	Measured	
2760	t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [source:swissprot;acc:q16559]	Ranked	
2760	t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [source:swissprot;acc:q16559]	Squared	
2760	t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [source:swissprot;acc:q16559]	Rooted	
2761	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [source:swissprot;acc:q9byb4]	Measured	
2761	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [source:swissprot;acc:q9byb4]	Ranked	
2761	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [source:swissprot;acc:q9byb4]	Squared	
2761	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [source:swissprot;acc:q9byb4]	Rooted	
2762	developmentally regulated gtp-binding protein 1 (drg 1). [source:swissprot;acc:q9y295]	Measured	
2762	developmentally regulated gtp-binding protein 1 (drg 1). [source:swissprot;acc:q9y295]	Ranked	
2762	developmentally regulated gtp-binding protein 1 (drg 1). [source:swissprot;acc:q9y295]	Squared	
2762	developmentally regulated gtp-binding protein 1 (drg 1). [source:swissprot;acc:q9y295]	Rooted	
2763	ring finger protein 3. [source:refseq;acc:nm_006315]	Measured	
2763	ring finger protein 3. [source:refseq;acc:nm_006315]	Ranked	
2763	ring finger protein 3. [source:refseq;acc:nm_006315]	Squared	
2763	ring finger protein 3. [source:refseq;acc:nm_006315]	Rooted	
2764	ras-related protein rab-11b (gtp-binding protein ypt3). [source:swissprot;acc:q15907]	Measured	
2764	ras-related protein rab-11b (gtp-binding protein ypt3). [source:swissprot;acc:q15907]	Ranked	
2764	ras-related protein rab-11b (gtp-binding protein ypt3). [source:swissprot;acc:q15907]	Squared	
2764	ras-related protein rab-11b (gtp-binding protein ypt3). [source:swissprot;acc:q15907]	Rooted	
2765	histone h2a.e (h2a/e). [source:swissprot;acc:q99878]	Measured	
2765	histone h2a.e (h2a/e). [source:swissprot;acc:q99878]	Ranked	
2765	histone h2a.e (h2a/e). [source:swissprot;acc:q99878]	Squared	
2765	histone h2a.e (h2a/e). [source:swissprot;acc:q99878]	Rooted	
2766	ss18-like protein 1 (syt homolog-1). [source:swissprot;acc:o75177]	Measured	
2766	ss18-like protein 1 (syt homolog-1). [source:swissprot;acc:o75177]	Ranked	
2766	ss18-like protein 1 (syt homolog-1). [source:swissprot;acc:o75177]	Squared	
2766	ss18-like protein 1 (syt homolog-1). [source:swissprot;acc:o75177]	Rooted	
2767	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [source:swissprot;acc:p02261]	Measured	
2767	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [source:swissprot;acc:p02261]	Ranked	
2767	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [source:swissprot;acc:p02261]	Squared	
2767	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [source:swissprot;acc:p02261]	Rooted	
2768	histone h2a.x (h2a/x). [source:swissprot;acc:p16104]	Measured	
2768	histone h2a.x (h2a/x). [source:swissprot;acc:p16104]	Ranked	

Legend:
- Rank is the rank after comparing the two networks
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.

- http://analysis.yellowcouch.org/