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

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Showing element 451 to 500 of 66312 in total

Filtered	1

Rank	description	Network Comparison Type	Interaction Map	Value Type	red	green	network_comparison	
29	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	Divided	Low confidence	Ranked	203.115	170.557	1.19089	
29	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Subtracted	Low confidence	Squared	92930.5	71802.4	21128.1	
29	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Divided	Low confidence	Rooted	48.8531	56.7071	1.16077	
29	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [source:swissprot;acc:q9uk08]	Divided	High confidence	Measured	1834.52	895.507	2.04858	
29	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [source:swissprot;acc:p19086]	Subtracted	High confidence	Ranked	267.139	336.075	68.936	
29	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	Divided	Low confidence	Squared	82347.8	61881.5	1.33073	
29	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Subtracted	High confidence	Measured	23693.7	18263	5430.7	
29	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]	Subtracted	High confidence	Squared	219048	129762	89286	
29	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	Divided	High confidence	Rooted	26.0288	43.1914	1.65937	
29	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Subtracted	High confidence	Rooted	210.928	192.165	18.763	
29	retinoblastoma-associated factor 600. [source:refseq;acc:nm_020765]	Subtracted	Low confidence	Rooted	76.5734	88.6244	12.051	
29	septin 10 isoform 1. [source:refseq;acc:nm_144710]	Subtracted	Low confidence	Measured	13081.2	14872.6	1791.4	
29	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Divided	Low confidence	Measured	3121.28	3739.84	1.19818	
29	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	Divided	High confidence	Ranked	187.458	243.678	1.29991	
30	bcl2-related ovarian killer. [source:refseq;acc:nm_032515]	Divided	Low confidence	Ranked	265.638	223.235	1.18995	
30	bestrophin (vitelliform macular dystrophy protein) (tu15b). [source:swissprot;acc:o76090]	Divided	Low confidence	Measured	36474.3	43509.4	1.19288	
30	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	Subtracted	High confidence	Rooted	60.8022	79.5099	18.7077	
30	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]	Divided	High confidence	Squared	143.692	457.521	3.18404	
30	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Divided	Low confidence	Rooted	48.8781	56.7253	1.16055	
30	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [source:swissprot;acc:p30670]	Divided	High confidence	Measured	1834.59	895.633	2.04837	
30	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [source:swissprot;acc:p19087]	Subtracted	High confidence	Ranked	267.14	336.075	68.935	
30	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476]	Subtracted	Low confidence	Squared	92930	71802.1	21127.9	
30	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Divided	Low confidence	Squared	82347.8	61881.5	1.33073	
30	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Subtracted	High confidence	Measured	23693.7	18263	5430.7	
30	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	Divided	High confidence	Rooted	26.0288	43.1914	1.65937	
30	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [source:swissprot;acc:q07326]	Subtracted	Low confidence	Measured	3278	5058.5	1780.5	
30	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	Subtracted	Low confidence	Rooted	44.4168	55.937	11.5202	
30	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [source:swissprot;acc:q00007]	Divided	High confidence	Ranked	187.457	243.678	1.29991	
30	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [source:swissprot;acc:p18583]	Subtracted	Low confidence	Ranked	255.382	223.538	31.844	
30	trophinin. [source:swissprot;acc:q12816]	Subtracted	High confidence	Squared	219048	129762	89286	
31	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Divided	Low confidence	Rooted	145.551	168.796	1.1597	
31	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Subtracted	High confidence	Squared	106226	192141	85915	
31	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	Subtracted	Low confidence	Ranked	142	170	28	
31	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Divided	High confidence	Squared	9924.76	25146.6	2.53372	
31	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Subtracted	Low confidence	Squared	92920.4	71796.4	21124	
31	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Divided	Low confidence	Ranked	57.395	48.8186	1.17568	
31	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [source:swissprot;acc:p50151]	Divided	High confidence	Measured	1834.63	895.697	2.04827	
31	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [source:swissprot;acc:p11488]	Subtracted	High confidence	Ranked	267.14	336.075	68.935	
31	histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [source:swissprot;acc:p49773]	Subtracted	Low confidence	Rooted	67.7094	56.875	10.8344	
31	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Subtracted	High confidence	Measured	23693.7	18263	5430.7	
31	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	Divided	Low confidence	Squared	82347.8	61881.5	1.33073	
31	n33 protein. [source:swissprot;acc:q13454]	Subtracted	Low confidence	Measured	3278	5058.5	1780.5	
31	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Subtracted	High confidence	Rooted	40.0958	58.7986	18.7028	
31	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	Divided	High confidence	Rooted	26.0288	43.1914	1.65937	
31	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [source:swissprot;acc:q00005]	Divided	High confidence	Ranked	187.458	243.677	1.2999	
31	vitelliform macular dystrophy 2-like protein 2. [source:refseq;acc:nm_153274]	Divided	Low confidence	Measured	36469.3	43503.3	1.19287	
32	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Divided	High confidence	Squared	9924.76	25146.6	2.53372	
32	cytohesin 4. [source:swissprot;acc:q9uia0]	Subtracted	Low confidence	Squared	92262.9	71400.2	20862.7	
32	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [source:swissprot;acc:q15485]	Divided	High confidence	Rooted	26.0288	43.1914	1.65937	
32	gbp protein isoform a. [source:refseq;acc:nm_017870]	Subtracted	High confidence	Rooted	23.9771	42.4773	18.5002	

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/