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

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Showing element 3180 to 3229 of 38536 in total

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Network Comparison Type  : Divided

green	network_comparison	Value Type	Interaction Map	Rank	red	description
2804	1.7602	Measured	High confidence	69	1593	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]
			Low confidence	77
2814.85	1.05986			500	2983.35	phosphoinositide-3-kinase, regulatory subunit 4, p150; phosphatidylinositol 3-kinase-associated p150. [refseq;acc:nm_014602]
2821.67	1.26419			153	2232	candidate tumor suppressor protein. [refseq;acc:nm_020381]
				154		supervillin isoform 1; membrane-associated f-actin binding protein p205; archvillin. [refseq;acc:nm_003174]
2827.2	1.01529			719	2784.62	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]
2833.94	1.09994		High confidence	311	3117.17	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]
2837.1	1.05861		Low confidence	510	2680.03	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]
2837.61	1.05818			512	3002.7	brain protein 16. [refseq;acc:nm_016458]
2853.65	1.0252		High confidence	438	2925.57	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]
2855.83	1.01872	Squared	Low confidence	747	2909.3	keratin associated protein 9.2. [refseq;acc:nm_031961]
2856.96	1.0185			752	2909.82	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]
				753		keratin associated protein 1.5. [refseq;acc:nm_031957]
				754		keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
2856.97				750	2909.83	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]
				751	2909.82	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]
				755		keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]
2857	1.01849			757	2909.84	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]
				758		keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]
				759		keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]
2857.01				756		similar to peptidylprolyl isomerase a (cyclophilin a); cyclophilin-lc; cyclophilin homolog overexpressed in liver cancer; chromosome 1 amplified sequence 2. [refseq;acc:nm_178230]
				760		star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]
2858.29	1.01824			761	2910.43	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]
2860.17	1.03791	Measured		595	2968.59	mitogen-activated protein kinase kinase kinase 3 (ec 2.7.1.-) (mapk/erk kinase kinase 3) (mek kinase 3) (mekk 3). [swissprot;acc:q99759]
2863.29	1.23762	Squared		246	3543.66	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]
2864.68	1.05571	Measured	High confidence	373	2713.5	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]
2864.71	1.16602	Squared	Low confidence	310	2456.82	dynactin 1 (150 kda dynein-associated polypeptide) (dp-150) (dap-150) (p150-glued) (p135). [swissprot;acc:q14203]
2869.96	1.11579		High confidence	374	2572.14	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]
2873.96	1.00101			491	2871.07	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]
2876	1.02191	Ranked		448	2939	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]
			Low confidence	674
2876.19	1.05232	Measured		552	2733.19	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]
2877.82	1.05288			549	2733.29	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]
2879.55	1.01735		High confidence	447	2929.51	40s ribosomal protein s3a. [swissprot;acc:p49241]
2887.65	1.01275		Low confidence	747	2851.31	protein cgi-147. [swissprot;acc:q9y3e5]
2888.82	1.25767	Squared		239	3633.18	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]
2896.88	1.05011	Measured		565	2758.64	huntingtin interacting protein c. [refseq;acc:nm_012272]
2923.92	1.03449		High confidence	412	3024.78	60s ribosomal protein l39. [swissprot;acc:p02404]
2924.8	1.0808			334	3161.12	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]
2941.38	1.01321		Low confidence	739	2980.23	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]
2942.86	1.07815			453	3172.85	beta tubulin 1, class vi. [refseq;acc:nm_030773]
2947.56	1.01073			766	2916.26	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]
2957.12	1.12829		High confidence	264	3336.48	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]
2987.56	1.08935		Low confidence	422	2742.51	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]
2993	1.13404	Squared		353	3394.17	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]
2998.91	1.07792	Measured		455	3232.58	tubulin beta-4q chain. [swissprot;acc:q99867]
3003.92	1.16417	Squared		312	2580.3	ebna-2 co-activator (100kd). [refseq;acc:nm_014390]
3010.22	1.11547	Measured	High confidence	285	2698.62	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]
3022.35	1.00108	Squared	Low confidence	832	3025.6	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]
3025.5	1.01344			781	3066.15	tera protein. [refseq;acc:nm_021238]

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.