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

Results: HTML CSV LaTeX

Showing element 1 to 16 of 16 in total

Rank  : 22
Interaction Map  : High confidence

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

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.