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

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Showing element 101 to 150 of 8289 in total

Filtered  : 1
Network Comparison Type  : Divided
Value Type  : Ranked

Rank	description	Interaction Map	green	network_comparison	red
51	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Low confidence	260.98	1.11149	234.802
	spermatogenesis associated 6. [refseq;acc:nm_019073]	High confidence	105	1.26667	133
52	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	Low confidence	260.98	1.11149	234.802
53	db83 protein. [swissprot;acc:p57088]
	transcription factor jun-b. [swissprot;acc:p17275]	High confidence	158.868	1.26611	201.144
54	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Low confidence	240.822	1.11056	267.448
	transcription factor jun-d. [swissprot;acc:p17535]	High confidence	158.941	1.26425	200.941
55	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Low confidence	240.78	1.11046	267.376
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	High confidence	254.434	1.26134	320.927
56	brachyury protein (t protein). [swissprot;acc:o15178]	Low confidence	202.592	1.11022	224.922
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	High confidence	336.233	1.25998	266.856
57	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Low confidence	182.73	1.10985	202.802
58	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	High confidence	336.191	1.25979	266.863
	jun dimerization protein. [refseq;acc:nm_130469]	Low confidence	182.73	1.10985	202.802
59	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	High confidence	336.19	1.25978	266.863
	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]	Low confidence	210.267	1.10875	233.134
60	fos-related antigen 2. [swissprot;acc:p15408]		182.961	1.10839	202.793
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	High confidence	336.184	1.25976	266.864
61	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]		336.182	1.25975
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Low confidence	182.974	1.10831	202.792
62	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		183.017	1.10804	202.79
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	High confidence	336.181	1.25974	266.865
63	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]		336.178	1.25973
	putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]	Low confidence	239.902	1.10749	265.688
64	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	High confidence	336.159	1.25965	266.868
	transcription factor jun-d. [swissprot;acc:p17535]	Low confidence	183.361	1.10552	202.709
65	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	High confidence	336.077	1.25807	267.136
	transcription factor jun-b. [swissprot;acc:p17275]	Low confidence	183.388	1.10546	202.728
66	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	High confidence	336.077	1.25807	267.136
	mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749]	Low confidence	200.783	1.10518	221.902
67	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	High confidence	336.075	1.25805	267.14
	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]	Low confidence	149.799	1.10505	165.535
68	60s ribosomal protein l37a. [swissprot;acc:p12751]		217.005	1.10455	239.692
	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	High confidence	336.075	1.25805	267.139
69	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]				267.14
	testis-specific protein tex28. [swissprot;acc:o15482]	Low confidence	235.017	1.10425	259.517
70	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	High confidence	336.074	1.25804	267.142
71	cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238]	Low confidence	209.149	1.10421	230.944
	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	High confidence	336.073	1.25802	267.144
72	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]
	set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197]	Low confidence	209.149	1.10421	230.944
73	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	High confidence	362	1.25694	288
	set and mynd domain containing protein 1. [sptrembl;acc:q8nb12]	Low confidence	209.149	1.10421	230.944
74	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	High confidence	362	1.25694	288
	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]	Low confidence	215.516	1.1006	195.817
75	nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323]		226.944	1.10031	249.709
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	High confidence	362	1.25694	288

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.