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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 323 to 372 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
21	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Rooted	Divided	0	36.9188	6.85565	5.38516
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		Subtracted	1	153.602	133.195	20.407
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Measured	Divided		677.5	1865.5	2.75351
		Squared			108.641	823.69	7.58176
	gbp protein isoform a. [refseq;acc:nm_017870]	Ranked	Subtracted		325.586	256.492	69.094
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Rooted	Divided		40.3337	24.2744	1.66157
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Ranked	Subtracted	0	14592	21113.7	6521.7
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Measured		1	23693.7	18263	5430.7
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Squared			219048	129762	89286
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Ranked	Divided		185.678	245.247	1.32082
	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]	Squared		0	0.0236686	5.76	243.36
	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	Measured	Subtracted		6804.88	5690.63	1114.25
		Squared			40674.4	28034.4	12640
	syntaxin 10 (syn10). [swissprot;acc:o60499]	Measured	Divided		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

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.