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 red green network_comparison

Results: HTML CSV LaTeX

Showing element 175 to 224 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
44	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	Rooted	40.5691	25.4263	1.59556	
44	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [source:swissprot;acc:p04901]	Measured	1931.34	1057.39	1.82652	
45	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Squared	129597	73157.5	1.77148	
45	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	Measured	1926.69	1056.02	1.82448	
45	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [source:swissprot;acc:p16520]	Rooted	40.081	25.1546	1.59339	
45	protein fosb (g0/g1 switch regulatory protein 3). [source:swissprot;acc:p53539]	Ranked	204.641	161.051	1.27066	
46	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	Squared	129597	73157.5	1.77148	
46	deltex 2. [source:refseq;acc:nm_020892]	Rooted	27.634	43.9629	1.5909	
46	fos-related antigen 1 (fra-1). [source:swissprot;acc:p15407]	Ranked	204.642	161.068	1.27053	
46	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	Measured	779.167	1390.33	1.78438	
47	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	Measured	779.167	1390.33	1.78438	
47	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Rooted	27.7078	44.017	1.58861	
47	gbp protein isoform a. [source:refseq;acc:nm_017870]	Ranked	325.586	256.492	1.26938	
47	ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	Squared	98517.9	56927.2	1.73059	
48	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	Measured	779.167	1390.33	1.78438	
48	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Ranked	65.4586	83.0461	1.26868	
48	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	Squared	6300.2	10703.5	1.69891	
48	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [source:refseq;acc:nm_018492]	Rooted	27.7254	44.0299	1.58807	
49	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	Squared	28994.2	17134.8	1.69212	
49	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Ranked	133	105	1.26667	
49	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	Rooted	27.7254	44.0299	1.58807	
49	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Measured	779.167	1390.33	1.78438	
50	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Ranked	133	105	1.26667	
50	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	Rooted	27.7254	44.0299	1.58807	
50	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	Measured	779.167	1390.33	1.78438	
50	putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm_014453]	Squared	28994.2	17134.8	1.69212	
51	associated molecule with the sh3 domain of stam. [source:refseq;acc:nm_006463]	Squared	28994.2	17134.8	1.69212	
51	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	Rooted	27.7254	44.0299	1.58807	
51	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Measured	779.167	1390.33	1.78438	
51	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Ranked	133	105	1.26667	
52	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Ranked	133	105	1.26667	
52	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	Measured	779.167	1390.33	1.78438	
52	neuralized-like. [source:refseq;acc:nm_004210]	Rooted	27.9107	44.1656	1.58239	
52	neuroendocrine differentiation factor; comparative gene identification transcript 149. [source:refseq;acc:nm_016079]	Squared	28994.2	17134.8	1.69212	
53	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [source:swissprot;acc:o14519]	Measured	779.167	1390.33	1.78438	
53	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [source:swissprot;acc:o43181]	Rooted	30.8986	46.4619	1.50369	
53	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Squared	28994.2	17134.8	1.69212	
53	transcription factor jun-b. [source:swissprot;acc:p17275]	Ranked	201.144	158.868	1.26611	
54	deltex 2. [source:refseq;acc:nm_020892]	Measured	1618.84	2651.88	1.63814	
54	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	Squared	219048	129762	1.68808	
54	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Rooted	40.0958	58.7986	1.46645	
54	transcription factor jun-d. [source:swissprot;acc:p17535]	Ranked	200.941	158.941	1.26425	
55	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Measured	1629.21	2662.12	1.63399	
55	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	Squared	219048	129762	1.68808	
55	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	Rooted	41.6734	28.9323	1.44038	
55	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	Ranked	320.927	254.434	1.26134	
56	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [source:swissprot;acc:p32929]	Rooted	41.6851	28.9509	1.43986	
56	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	Ranked	266.856	336.233	1.25998	
56	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Squared	219048	129762	1.68808	
56	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [source:refseq;acc:nm_018492]	Measured	1631.67	2664.55	1.63302	

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/