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 - 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.

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 451 to 500 of 66312 in total

Filtered  : 1

Rank	description	Value Type	Network Comparison Type	Interaction Map	red	green	network_comparison
29	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Ranked	Divided	Low confidence	203.115	170.557	1.19089
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Squared	Subtracted		92930.5	71802.4	21128.1
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Rooted	Divided		48.8531	56.7071	1.16077
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Measured		High confidence	1834.52	895.507	2.04858
	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	Ranked	Subtracted		267.139	336.075	68.936
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Squared	Divided	Low confidence	82347.8	61881.5	1.33073
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Measured	Subtracted	High confidence	23693.7	18263	5430.7
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Squared			219048	129762	89286
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Rooted	Divided		26.0288	43.1914	1.65937
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		Subtracted		210.928	192.165	18.763
	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]			Low confidence	76.5734	88.6244	12.051
	septin 10 isoform 1. [refseq;acc:nm_144710]	Measured			13081.2	14872.6	1791.4
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]		Divided		3121.28	3739.84	1.19818
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Ranked		High confidence	187.458	243.678	1.29991
30	bcl2-related ovarian killer. [refseq;acc:nm_032515]			Low confidence	265.638	223.235	1.18995
	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Measured			36474.3	43509.4	1.19288
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Rooted	Subtracted	High confidence	60.8022	79.5099	18.7077
	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	Squared	Divided		143.692	457.521	3.18404
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Rooted		Low confidence	48.8781	56.7253	1.16055
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Measured		High confidence	1834.59	895.633	2.04837
	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Ranked	Subtracted		267.14	336.075	68.935
	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). [swissprot;acc:o60476]	Squared		Low confidence	92930	71802.1	21127.9
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]		Divided		82347.8	61881.5	1.33073
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Measured	Subtracted	High confidence	23693.7	18263	5430.7
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Rooted	Divided		26.0288	43.1914	1.65937
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	Measured	Subtracted	Low confidence	3278	5058.5	1780.5
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Rooted			44.4168	55.937	11.5202
	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). [swissprot;acc:q00007]	Ranked	Divided	High confidence	187.457	243.678	1.29991
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]		Subtracted	Low confidence	255.382	223.538	31.844
	trophinin. [swissprot;acc:q12816]	Squared		High confidence	219048	129762	89286
31	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]				106226	192141	85915
		Rooted	Divided	Low confidence	145.551	168.796	1.1597
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Ranked	Subtracted		142	170	28
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Squared	Divided	High confidence	9924.76	25146.6	2.53372
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		Subtracted	Low confidence	92920.4	71796.4	21124
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Ranked	Divided		57.395	48.8186	1.17568
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	Measured		High confidence	1834.63	895.697	2.04827
	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	Ranked	Subtracted		267.14	336.075	68.935
	histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773]	Rooted		Low confidence	67.7094	56.875	10.8344
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Measured		High confidence	23693.7	18263	5430.7
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Squared	Divided	Low confidence	82347.8	61881.5	1.33073
	n33 protein. [swissprot;acc:q13454]	Measured	Subtracted		3278	5058.5	1780.5
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Rooted		High confidence	40.0958	58.7986	18.7028
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]		Divided		26.0288	43.1914	1.65937
	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). [swissprot;acc:q00005]	Ranked			187.458	243.677	1.2999
	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	Measured		Low confidence	36469.3	43503.3	1.19287
32	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Squared		High confidence	9924.76	25146.6	2.53372
	cytohesin 4. [swissprot;acc:q9uia0]		Subtracted	Low confidence	92262.9	71400.2	20862.7
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Rooted	Divided	High confidence	26.0288	43.1914	1.65937
	gbp protein isoform a. [refseq;acc:nm_017870]		Subtracted		23.9771	42.4773	18.5002

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.