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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

Results: HTML CSV LaTeX

Showing element 1858 to 1907 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Hugo	Value Type	red	green	network_comparison
465	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]	AKT2	Rooted	50.2317	55.0025	1.09498
	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	E2F1	Measured	3847.31	4409.22	1.14605
	trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646]	TRIT1	Squared	25310.2	30537	1.20651
466	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	ADCY6	Ranked	248.152	267.226	1.07686
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	ATP2C2	Squared	25513.6	30779.5	1.2064
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	E2F2	Measured	3847.31	4409.22	1.14605
	vav-3 protein. [swissprot;acc:q9ukw4]	VAV3	Rooted	66.089	72.3555	1.09482
467	40s ribosomal protein s5. [swissprot;acc:p46782]	RPS5		50.4649	46.1093	1.09446
	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	ADCY5	Ranked	248.152	267.226	1.07686
	metastasis-associated protein mta1. [swissprot;acc:q13330]	MTA1	Measured	4864.25	5573.62	1.14583
	nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818]	NUCB1	Squared	23531.7	28371.6	1.20568
468	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	RBBP4	Measured	4869.15	5578.02	1.14558
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	MLH1	Squared	23531.7	28371.6	1.20568
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	LRRC15	Ranked	248.152	267.226	1.07686
	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	CCT3	Rooted	107.178	117.276	1.09422
469	60s ribosomal protein l9. [swissprot;acc:p32969]	no value		51.1334	46.7335	1.09415
	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	FEM1B	Ranked	248.152	267.226	1.07686
	nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303]	NUCB2	Squared	23531.7	28371.6	1.20568
	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	NOL1	Measured	3831.17	4388.74	1.14554
470	block of proliferation 1. [swissprot;acc:q14137]	BOP1		3796.24	4348.59	1.1455
	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	LRRC3	Ranked	248.152	267.226	1.07686
	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	SNW1	Rooted	60.0148	65.6429	1.09378
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	PPP2R1B	Squared	10418.3	8641.84	1.20557
471	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]	LAMC1	Ranked	248.152	267.226	1.07686
	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778]	MAPK11	Measured	9649.61	11053.5	1.14549
	phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205]	PGK2	Squared	28188.7	33982.7	1.20554
	vav-2 protein. [swissprot;acc:p52735]	VAV2	Rooted	66.088	72.2597	1.09339
472	gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104]	ENO2	Squared	28190.4	33984.1	1.20552
	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]	SPHK1	Measured	9649.61	11053.5	1.14549
	thymic stromal co-transporter. [refseq;acc:nm_033051]	SLC46A2	Ranked	248.152	267.226	1.07686
	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	PUS1	Rooted	50.3767	46.0753	1.09336
473	beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]	ENO3	Squared	28190.4	33984.1	1.20552
	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	PRPF31	Ranked	225.661	209.651	1.07637
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	SEPHS2	Rooted	62.574	68.4128	1.09331
	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]	DPAGT1	Measured	9649.61	11053.5	1.14549
474	alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733]	ENO1	Squared	28190.4	33984.1	1.20552
	flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]	MICAL2	Rooted	62.574	68.4128	1.09331
	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	KCNA2	Ranked	226.789	210.818	1.07576
	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]	DLC1	Measured	9649.61	11053.5	1.14549
475	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866]	INPP4B	Rooted	62.574	68.4128	1.09331
	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]	MAPKAPK2	Measured	9649.61	11053.5	1.14549
	phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558]	PGK1	Squared	28192	33985.3	1.20549
	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470]	KCNA1	Ranked	226.727	210.816	1.07547
476	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]	CHRNA6	Measured	9649.61	11053.5	1.14549
	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459]	KCNA4	Ranked	226.681	210.814	1.07527
	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903]	SEPHS1	Rooted	62.574	68.4128	1.09331
	vav proto-oncogene. [swissprot;acc:p15498]	VAV1	Squared	31223.8	37614.3	1.20467
477	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566]	INPP4A	Rooted	62.574	68.4128	1.09331
	nitrogen fixation cluster-like. [refseq;acc:nm_014301]	ISCU	Measured	9649.61	11053.5	1.14549
	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	NIP7	Ranked	251.926	234.547	1.0741

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
- Hugo is the HGNC identifier if it exists
- 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.