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	Interaction Map	Network Comparison Type	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	description	Value Type	Network Comparison Type	red	green	network_comparison
19	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Squared	Divided	108.641	823.69	7.58176
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Rooted		25.6987	43.561	1.69507
20	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
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Measured		23421.5	17580.4	5841.1
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Ranked	Divided	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
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Rooted	Divided	40.3337	24.2744	1.66157
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Squared	Subtracted	219048	129762	89286
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Measured	Divided	677.5	1865.5	2.75351
		Squared		108.641	823.69	7.58176
21	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Rooted	Subtracted	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
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Measured	Subtracted	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
22	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Rooted		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
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Ranked		58	44	1.31818
	gbp protein isoform a. [refseq;acc:nm_017870]	Measured		699.76	1894.39	2.7072
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	Rooted		40.3358	24.2919	1.66046
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Measured	Subtracted	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
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Squared	Divided	143.692	457.521	3.18404
24	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Rooted	Subtracted	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
	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
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Ranked	Divided	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
25	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Squared	Divided	143.692	457.521	3.18404
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Ranked	Subtracted	322	253	69
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Rooted	Divided	40.3361	24.295	1.66026
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Measured		1833.01	892.67	2.0534
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Squared	Subtracted	219048	129762	89286
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Measured		23693.7	18263	5430.7
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Rooted		146.94	167.046	20.106
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Ranked	Divided	58	44	1.31818

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.