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

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Showing element 151 to 200 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	Value Type	description	Filtered	red	green	network_comparison
19	Rooted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	0	9.20014	60.0707	6.52932
		protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	1	25.6987	43.561	1.69507
20	Measured	ero1-like. [refseq;acc:nm_014584]	0	82	0.00001	8200000
		protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	1	677.5	1865.5	2.75351
	Ranked	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]		185.678	245.247	1.32082
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	22286	13216	1.68629
	Squared	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]		23.4957	0.0297673	789.312
		protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	1	108.641	823.69	7.58176
	Rooted	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	0	11.3774	1.80368	6.30788
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	1	40.3337	24.2744	1.66157
21	Measured	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]		677.5	1865.5	2.75351
		syntaxin 10 (syn10). [swissprot;acc:o60499]	0	118.878	17.6611	6.73106
	Ranked	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]		6313.38	10621.4	1.68236
		myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	1	185.678	245.247	1.32082
	Squared	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]		108.641	823.69	7.58176
		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]	0	0.0236686	5.76	243.36
	Rooted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		36.9188	6.85565	5.38516
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	1	40.3337	24.2744	1.66157
22	Measured	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	1865.5	2.75351
		similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0	60	0.00001	6000000
	Ranked	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	1	185.678	245.247	1.32082
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0	20989	12479	1.68195
	Squared	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	1	108.641	823.69	7.58176
		protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	0	0.000236686	0.0532544	225
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	1	40.3357	24.2915	1.66049
		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]	0	3.16228	12.49	3.94968
23	Measured	gbp protein isoform a. [refseq;acc:nm_017870]	1	699.76	1894.39	2.7072
		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). [swissprot;acc:q9byb4]	0	0.00001	59	5900000
	Ranked	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	1	58	44	1.31818
		hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	0	15520.4	9285.44	1.67148
	Squared	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		174.646	0.796213	219.346
		neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	1	143.692	457.521	3.18404
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]		40.3358	24.2919	1.66046
		protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	0	1	3.87298	3.87298
24	Measured	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	1	950.561	2108.52	2.21818
		ptd016 protein. [refseq;acc:nm_016125]	0	30	158	5.26667
	Ranked	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		13730.5	8257	1.66289
		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	1	58	44	1.31818
	Squared	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]		143.692	457.521	3.18404
		cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	0	4.16226	0.02001	208.009
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	1	40.336	24.2941	1.66032
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	29.3087	7.61577	3.84842
25	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	1	1833.01	892.67	2.0534
		potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	0	148	773	5.22297
	Ranked	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]		13730.5	8257	1.66289
		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	1	58	44	1.31818
	Squared	60s ribosomal protein l37a. [swissprot;acc:p12751]	0	44.3683	0.344399	128.828
		doc-1 related protein (doc-1r). [swissprot;acc:o75956]	1	143.692	457.521	3.18404
	Rooted	60s ribosomal protein l37a. [swissprot;acc:p12751]	0	13.7805	3.80565	3.62106
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	1	40.3361	24.295	1.66026

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.