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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 194 to 243 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
97	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	0	8335.82	10228.3	1.22703	
98	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	1	88.2482	110.265	1.24949	
98	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [source:swissprot;acc:q9y466]	0	7234.6	8858.94	1.22452	
99	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	1	88.2482	110.265	1.24949	
99	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	0	12787.8	10454.7	1.22316	
100	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [source:swissprot;acc:p12532]	0	9183.49	11217.7	1.22151	
100	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	1	88.2482	110.265	1.24949	
101	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	0	14548.5	11915.2	1.221	
101	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	1	88.2482	110.265	1.24949	
102	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	0	12738.7	10437.1	1.22052	
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]	1	88.2482	110.265	1.24949	
103	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	0	7495.26	9130.38	1.21815	
103	trophinin. [source:swissprot;acc:q12816]	1	88.2482	110.265	1.24949	
104	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	1	252.371	202.016	1.24926	
104	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [source:swissprot;acc:q15765]	0	9545	7868	1.21314	
105	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [source:swissprot;acc:p45954]	0	17410.5	14360	1.21243	
105	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [source:swissprot;acc:p04901]	1	266.716	333.165	1.24914	
106	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [source:swissprot;acc:p43897]	0	16290.7	13464.8	1.20987	
106	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	1	252.329	202.004	1.24913	
107	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	1	252.309	201.998	1.24907	
107	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	0	11853.5	9808.86	1.20845	
108	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	1	252.296	201.995	1.24902	
108	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [source:swissprot;acc:p32322]	0	10585.3	12769.1	1.2063	
109	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4w2]	0	14466.8	12031.7	1.20239	
109	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	1	266.933	333.281	1.24856	
110	deltex 2. [source:refseq;acc:nm_020892]	1	333.144	267.393	1.2459	
110	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [source:swissprot;acc:q02880]	0	12584.5	10470.6	1.20189	
111	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	1	332.925	267.274	1.24563	
111	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [source:swissprot;acc:p18031]	0	9940.69	11929	1.20002	
112	40s ribosomal protein s26. [source:swissprot;acc:p02383]	0	14269.7	17098	1.1982	
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]	1	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]	1	332.874	267.246	1.24557	
113	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	0	5673.33	6797.56	1.19816	
114	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [source:swissprot;acc:p54132]	0	8871.11	10603.2	1.19525	
114	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	1	332.874	267.246	1.24557	
115	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	1	332.874	267.246	1.24557	
115	spir-2 protein (fragment). [source:sptrembl;acc:q8wwl2]	0	18662.8	15627	1.19427	
116	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [source:swissprot;acc:p16520]	1	268.565	334.483	1.24545	
116	metaxin 1. [source:swissprot;acc:q13505]	0	13761.3	16422.1	1.19335	
117	basic proline-rich peptide p-e (ib-9). [source:swissprot;acc:p02811]	0	11545	13771.5	1.19285	
117	neuralized-like. [source:refseq;acc:nm_004210]	1	332.326	266.948	1.24491	
118	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [source:swissprot;acc:p41181]	0	12049	14370.7	1.19269	
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]	1	284.753	228.934	1.24382	
119	mesoderm induction early response 1. [source:refseq;acc:nm_020948]	0	3609	4302.5	1.19216	
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]	1	318.982	259.004	1.23157	
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]	1	269.278	327.709	1.21699	
120	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	0	5797	4873	1.18962	
121	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [source:swissprot;acc:p32929]	1	269.254	327.655	1.2169	
121	zinc finger protein 232. [source:swissprot;acc:q9uny5]	0	11523.7	13686.9	1.18772	
122	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [source:refseq;acc:nm_004980]	1	269.248	327.642	1.21688	

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/