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.

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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 1673 to 1722 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
105	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	Ranked	Divided	1	266.716	333.165	1.24914
	musashi 1. [refseq;acc:nm_002442]	Measured			4241.57	5810.79	1.36996
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]		Subtracted		11068	8508.5	2559.5
	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	Squared			90432.9	56304.2	34128.7
	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]	Rooted			63.7477	48.1588	15.5889
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Ranked		0	11853.5	9808.86	2044.64
	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	Rooted			13.0525	17.6565	4.604
	transcription factor jun-d. [swissprot;acc:p17535]	Ranked		1	200.941	158.941	42
106	brain protein 16. [refseq;acc:nm_016458]			0	6890.54	4854.99	2035.55
	casein kinase i alpha s-like. [refseq;acc:nm_145203]	Squared			7795.92	9052.52	1256.6
	cytohesin 4. [swissprot;acc:q9uia0]		Divided	1	407289	263351	1.54656
	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897]	Ranked		0	16290.7	13464.8	1.20987
	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	Measured	Subtracted		712.071	416.524	295.547
	nostrin. [refseq;acc:nm_052946]	Ranked		1	209.299	249.187	39.888
	nuclear protein ukp68. [refseq;acc:nm_024824]	Measured	Divided		4241.57	5810.79	1.36996
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Rooted			60.8692	77.7165	1.27678
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Measured	Subtracted		11068	8508.5	2559.5
	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]	Squared	Divided	0	299.137	144.414	2.07139
	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]		Subtracted	1	82624.3	115061	32436.7
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Measured	Divided	0	1251.66	858.525	1.45792
	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	Rooted	Subtracted		13.0522	17.6559	4.6037
	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]		Divided		5.47723	7.07107	1.29099
	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	Ranked		1	252.329	202.004	1.24913
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Rooted	Subtracted		63.7477	48.1589	15.5888
107	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Measured	Divided		4266.04	5843.51	1.36977
	60s ribosomal protein l7. [swissprot;acc:p18124]		Subtracted	0	1915.27	2206.07	290.8
	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	Ranked			9183.49	11217.7	2034.21
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Squared	Divided	1	407289	263351	1.54656
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	Rooted	Subtracted	0	21.3244	25.9172	4.5928
	eap30 subunit of ell complex. [refseq;acc:nm_007241]	Ranked		1	209.299	249.187	39.888
	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	Rooted	Divided		60.875	77.7152	1.27664
	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Ranked			252.309	201.998	1.24907
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Measured		0	326.677	472.605	1.4467
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Rooted			22.2259	17.2182	1.29084
	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	Squared	Subtracted	1	84857.8	53402.4	31455.4
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]		Divided	0	4141.27	2000.69	2.06992
	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	Measured	Subtracted	1	14229.2	16780.7	2551.5
	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]	Rooted			63.7477	48.1594	15.5883
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Ranked	Divided	0	11853.5	9808.86	1.20845
	tubby protein homolog. [swissprot;acc:p50607]	Squared	Subtracted		9661.54	10902.9	1241.36
108	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Ranked			6742.5	8759.5	2017
	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Measured	Divided		292	421	1.44178
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Squared	Subtracted		1797.76	558.241	1239.52
	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	Rooted	Divided		13.7191	17.6786	1.28861
	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	Measured		1	4366.44	5899.76	1.35116
	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	Ranked			252.296	201.995	1.24902
	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]		Subtracted		209.299	249.187	39.888
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Measured		0	482.426	192.295	290.131
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Squared	Divided	1	19321	12542.6	1.54043
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Ranked		0	10585.3	12769.1	1.2063

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.