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

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Showing element 3180 to 3229 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

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

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.