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

Results: HTML CSV LaTeX

Showing element 1 to 16 of 16 in total

Rank  : 22
Filtered  : 1

Value Type	Interaction Map	description	Network Comparison Type	red	green	network_comparison
Measured	High confidence	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Subtracted	23693.7	18263	5430.7
		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	1865.5	2.75351
	Low confidence	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]		3126.88	3997.02	1.27828
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Subtracted	2399.5	543.5	1856
Ranked	High confidence	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Divided	185.678	245.247	1.32082
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Subtracted	322	253	69
	Low confidence	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]		210.241	246.125	35.884
		n33 protein. [swissprot;acc:q13454]	Divided	198	163	1.21472
Squared	High confidence	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Subtracted	219048	129762	89286
		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	823.69	7.58176
	Low confidence	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		80340.8	57685.7	1.39273
		retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Subtracted	122475	159767	37292
Rooted	High confidence	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Divided	40.3357	24.2915	1.66049
		microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Subtracted	153.578	133.176	20.402
	Low confidence	implantation-associated protein. [refseq;acc:nm_032121]	Divided	57.2538	71.1231	1.24224
		n33 protein. [swissprot;acc:q13454]	Subtracted			13.8693

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.