MK5 Microarray Data

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

Results: HTML CSV LaTeX

Showing element 1 to 16 of 16 in total

Interaction Map  : High confidence
Rank  : 22

Value Type	Network Comparison Type	green	Filtered	description	red	network_comparison
Measured	Divided	0.00001	0	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	60	6000000
		1865.5	1	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	677.5	2.75351
	Subtracted	18263		hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	23693.7	5430.7
		30022.4	0	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	31122	1099.6
Ranked	Divided	245.247	1	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	185.678	1.32082
		12479	0	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	20989	1.68195
	Subtracted	253	1	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	322	69
		11965.7	0	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	5510.5	6455.2
Squared	Divided	0.0532544		protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	0.000236686	225
		823.69	1	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	108.641	7.58176
	Subtracted	129762		melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	219048	89286
		204096	0	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	192242	11854
Rooted	Divided	12.49		succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	3.16228	3.94968
		24.2915	1	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	40.3357	1.66049
	Subtracted	13.5647	0	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	24.454	10.8893
		133.176	1	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	153.578	20.402

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.