Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 green red network_comparison

Results: HTML CSV LaTeX

Showing element 101 to 150 of 8289 in total

Value Type	Ranked
Network Comparison Type	Divided
Filtered	1

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

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/