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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 193 to 242 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
97	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [source:swissprot;acc:q02410]	Subtracted	271.752	225.68	46.072	
97	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Divided	88.2482	110.265	1.24949	
98	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Divided	88.2482	110.265	1.24949	
98	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [source:swissprot;acc:p01100]	Subtracted	204.641	160.957	43.684	
99	jun dimerization protein. [source:refseq;acc:nm_130469]	Subtracted	204.641	160.957	43.684	
99	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	Divided	88.2482	110.265	1.24949	
100	fos-related antigen 2. [source:swissprot;acc:p15408]	Subtracted	204.641	161.046	43.595	
100	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Divided	88.2482	110.265	1.24949	
101	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	Divided	88.2482	110.265	1.24949	
101	protein fosb (g0/g1 switch regulatory protein 3). [source:swissprot;acc:p53539]	Subtracted	204.641	161.051	43.59	
102	fos-related antigen 1 (fra-1). [source:swissprot;acc:p15407]	Subtracted	204.642	161.068	43.574	
102	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]	Divided	88.2482	110.265	1.24949	
103	transcription factor jun-b. [source:swissprot;acc:p17275]	Subtracted	201.144	158.868	42.276	
103	trophinin. [source:swissprot;acc:q12816]	Divided	88.2482	110.265	1.24949	
104	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	Divided	252.371	202.016	1.24926	
104	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Subtracted	256.228	298.438	42.21	
105	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [source:swissprot;acc:p04901]	Divided	266.716	333.165	1.24914	
105	transcription factor jun-d. [source:swissprot;acc:p17535]	Subtracted	200.941	158.941	42	
106	nostrin. [source:refseq;acc:nm_052946]	Subtracted	209.299	249.187	39.888	
106	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	Divided	252.329	202.004	1.24913	
107	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	Subtracted	209.299	249.187	39.888	
107	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Divided	252.309	201.998	1.24907	
108	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Divided	252.296	201.995	1.24902	
108	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	Subtracted	209.299	249.187	39.888	
109	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	Subtracted	209.299	249.187	39.888	
109	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	Divided	266.933	333.281	1.24856	
110	deltex 2. [source:refseq;acc:nm_020892]	Divided	333.144	267.393	1.2459	
110	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	Subtracted	209.299	249.187	39.888	
111	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Divided	332.925	267.274	1.24563	
111	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	Subtracted	209.299	249.187	39.888	
112	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Subtracted	275.754	235.908	39.846	
112	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]	Divided	332.874	267.246	1.24557	
113	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	Divided	332.874	267.246	1.24557	
113	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [source:swissprot;acc:p05323]	Subtracted	194.372	234.204	39.832	
114	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	Subtracted	229.818	267.265	37.447	
114	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	Divided	332.874	267.246	1.24557	
115	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Subtracted	277.546	240.461	37.085	
115	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	Divided	332.874	267.246	1.24557	
116	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [source:swissprot;acc:p16520]	Divided	268.565	334.483	1.24545	
116	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [source:refseq;acc:nm_006339]	Subtracted	208.52	171.595	36.925	
117	high-mobility group 20a. [source:refseq;acc:nm_018200]	Subtracted	208.588	171.778	36.81	
117	neuralized-like. [source:refseq;acc:nm_004210]	Divided	332.326	266.948	1.24491	
118	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]	Divided	284.753	228.934	1.24382	
118	odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	Subtracted	274.027	237.79	36.237	
119	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Subtracted	281.582	246.371	35.211	
119	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]	Divided	318.982	259.004	1.23157	
120	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Subtracted	227.199	192.715	34.484	
120	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	Divided	269.278	327.709	1.21699	
121	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [source:swissprot;acc:p32929]	Divided	269.254	327.655	1.2169	
121	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	Subtracted	227.202	192.823	34.379	

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/