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

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Showing element 336 to 385 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
21	syntaxin 10 (syn10). [swissprot;acc:o60499]	Measured	Divided	0	118.878	17.6611	6.73106
22	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Rooted	Subtracted		24.454	13.5647	10.8893
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Ranked	Divided	1	185.678	245.247	1.32082
	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	Squared	Subtracted	0	192242	204096	11854
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Rooted	Divided	1	40.3357	24.2915	1.66049
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Measured	Subtracted		23693.7	18263	5430.7
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Squared			219048	129762	89286
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Rooted			153.578	133.176	20.402
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Ranked			322	253	69
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Measured	Divided		677.5	1865.5	2.75351
		Squared			108.641	823.69	7.58176
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]			0	0.000236686	0.0532544	225
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Ranked			20989	12479	1.68195
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Measured			60	0.00001	6000000
	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]	Rooted			3.16228	12.49	3.94968
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Measured	Subtracted		31122	30022.4	1099.6
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Ranked			5510.5	11965.7	6455.2
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		Divided	1	58	44	1.31818
	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Measured	Subtracted	0	6596.23	5540.2	1056.03
	gbp protein isoform a. [refseq;acc:nm_017870]		Divided	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
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	Rooted		1	40.3358	24.2919	1.66046
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	Ranked		0	15520.4	9285.44	1.67148
			Subtracted				6234.96
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Measured		1	23693.7	18263	5430.7
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Squared			219048	129762	89286
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Ranked			322	253	69
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Rooted			153.578	133.176	20.402
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Squared	Divided	0	174.646	0.796213	219.346
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]			1	143.692	457.521	3.18404
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]		Subtracted	0	46977	36903.3	10073.7
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Rooted	Divided		1	3.87298	3.87298
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]		Subtracted		136.763	147.411	10.648
24	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Ranked	Divided		13730.5	8257	1.66289
	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Squared		1	143.692	457.521	3.18404
	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]			0	4.16226	0.02001	208.009
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Rooted	Subtracted	1	153.548	133.153	20.395
	fos-related antigen 2. [swissprot;acc:p15408]	Measured		0	3233.86	2208.1	1025.76
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Rooted	Divided	1	40.336	24.2941	1.66032
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Measured	Subtracted		23693.7	18263	5430.7
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Squared			219048	129762	89286
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Rooted		0	17.7955	7.34614	10.4494
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		Divided		29.3087	7.61577	3.84842
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Ranked		1	58	44	1.31818
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Measured			950.561	2108.52	2.21818
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Ranked	Subtracted		322	253	69
	ptd016 protein. [refseq;acc:nm_016125]	Measured	Divided	0	30	158	5.26667
	sedlin. [swissprot;acc:o14582]	Ranked	Subtracted		22440	16388	6052
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	Squared			21101.4	11769.5	9331.9
25	60s ribosomal protein l37a. [swissprot;acc:p12751]		Divided		44.3683	0.344399	128.828

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.