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

Results: HTML CSV LaTeX

Showing element 151 to 200 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	Network Comparison Type	red	green	network_comparison
19	Rooted	cytohesin 4. [swissprot;acc:q9uia0]	Subtracted	203.673	182.638	21.035
		protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Divided	25.6987	43.561	1.69507
20	Measured	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Subtracted	23421.5	17580.4	5841.1
		protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Divided	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
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Subtracted	266.868	336.159	69.291
	Squared	melanoma antigen, family b, 6. [refseq;acc:nm_173523]		219048	129762	89286
		protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Divided	108.641	823.69	7.58176
	Rooted	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Subtracted	203.673	182.638	21.035
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Divided	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
		melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Subtracted	23693.7	18263	5430.7
	Ranked	gbp protein isoform a. [refseq;acc:nm_017870]		325.586	256.492	69.094
		myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Divided	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
		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Subtracted	219048	129762	89286
	Rooted	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		153.602	133.195	20.407
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Divided	40.3337	24.2744	1.66157
22	Measured	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
	Ranked	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]		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
	Squared	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]		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
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]		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
23	Measured	gbp protein isoform a. [refseq;acc:nm_017870]	Divided	699.76	1894.39	2.7072
		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Subtracted	23693.7	18263	5430.7
	Ranked	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Divided	58	44	1.31818
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Subtracted	322	253	69
	Squared	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]		219048	129762	89286
		neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Divided	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
		microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Subtracted	153.578	133.176	20.402
24	Measured	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]		23693.7	18263	5430.7
		protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Divided	950.561	2108.52	2.21818
	Ranked	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]		58	44	1.31818
		protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Subtracted	322	253	69
	Squared	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Divided	143.692	457.521	3.18404
		melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Subtracted	219048	129762	89286
	Rooted	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]		153.548	133.153	20.395
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Divided	40.336	24.2941	1.66032
25	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]		1833.01	892.67	2.0534
		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Subtracted	23693.7	18263	5430.7
	Ranked	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]		322	253	69
		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Divided	58	44	1.31818
	Squared	doc-1 related protein (doc-1r). [swissprot;acc:o75956]		143.692	457.521	3.18404
		melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Subtracted	219048	129762	89286
	Rooted	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Divided	40.3361	24.295	1.66026
		myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Subtracted	146.94	167.046	20.106

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.