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

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Showing element 1780 to 1829 of 66312 in total

Filtered  : 1

Rank	Hugo	Network Comparison Type	Value Type	description	Interaction Map	red	green	network_comparison
112	CACNG5	Divided	Rooted	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	High confidence	49.3267	62.4167	1.26537
	CREG1		Ranked	cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]	Low confidence	197.762	212.013	1.07206
	CTPS2	Subtracted	Squared	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	High confidence	96730.5	69286.7	27443.8
	DLGAP4		Ranked	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]	Low confidence	197.779	211.983	14.204
	LASS2	Divided	Rooted	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]		71.084	76.8432	1.08102
	MAGEE2		Measured	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]		11285.3	10318.5	1.0937
	MYH3		Squared	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	High confidence	19321	12542.6	1.54043
	PBK		Ranked	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]		332.874	267.246	1.24557
	POLE4	Subtracted		dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]		275.754	235.908	39.846
	RASAL2		Rooted	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Low confidence	55.9786	61.8641	5.8855
	SLC16A5		Measured	monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375]		10351.8	11210.8	859
	SMPD2		Rooted	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	High confidence	33.9632	18.4255	15.5377
	SNRP70	Divided	Measured	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]		4366.44	5899.76	1.35116
113	no value			filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
				melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Low confidence	11285.3	10318.5	1.0937
	ARRB2		Rooted	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	High confidence	80.4705	101.526	1.26165
	ATF3	Subtracted	Measured	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]		4800.81	7132.71	2331.9
	BRP44		Squared	brain protein 44. [swissprot;acc:o95563]	Low confidence	62640.6	71038.3	8397.7
	CREG2	Divided	Ranked	cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]		197.763	212.011	1.07205
	CTPS	Subtracted	Squared	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	High confidence	96602.7	69211.2	27391.5
	KHDRBS3	Divided	Ranked	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]		332.874	267.246	1.24557
	MAN1B1		Rooted	endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7]	Low confidence	66.9562	72.3243	1.08017
	MYH1		Squared	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	High confidence	19321	12542.6	1.54043
	PPP2CA	Subtracted	Ranked	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]		194.372	234.204	39.832
	SEPT1	Divided	Squared	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	Low confidence	59884.7	68850.8	1.14972
	SLC11A2	Subtracted	Ranked	natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281]		224.763	210.566	14.197
	SLC16A1		Measured	monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985]		10348.5	11206.7	858.2
	TMEM33		Rooted	db83 protein. [swissprot;acc:p57088]	High confidence	33.9632	18.4255	15.5377
	VPS33B			vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267]	Low confidence	69.4249	75.2464	5.8215
114	no value	Divided	Squared	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	High confidence	19321	12542.6	1.54043
		Subtracted	Measured	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]		13768.2	11466	2302.2
	ARRB1	Divided	Rooted	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]		80.4705	101.526	1.26165
	ATG12	Subtracted	Squared	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]		67438.6	40697	26741.6
	B9D1		Ranked	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]		229.818	267.265	37.447
	DFFB		Rooted	dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075]	Low confidence	61.1174	66.8946	5.7772
	DLGAP1	Divided	Ranked	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490]		197.779	211.983	1.07182
	GNB5	Subtracted	Rooted	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	High confidence	40.225	24.7051	15.5199
	KHDRBS1	Divided	Ranked	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]		332.874	267.246	1.24557
	MAGEA11		Measured	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Low confidence	11285.3	10318.5	1.0937
	MRPS17	Subtracted	Ranked	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		58	44	14
	OTC	Divided	Squared	ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480]		65896.9	75670.5	1.14832
	PRPF40B		Measured	huntingtin interacting protein c. [refseq;acc:nm_012272]	High confidence	4300.47	5807.72	1.35048
	PSEN2		Rooted	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	Low confidence	66.9562	72.3243	1.08017
	SLC16A5	Subtracted	Squared	monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375]		62486.3	70725.6	8239.3
	SLC16A7		Measured	monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669]		10346.9	11204.8	857.9
115	no value			pnas-18. [sptrembl;acc:q9bzu3]	High confidence	13680.5	11409.6	2270.9
			Squared	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]		72886.3	98544.5	25658.2
	CPSF2	Divided		cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	Low confidence	59004.9	51446.9	1.14691
	DGCR14	Subtracted	Rooted	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	High confidence	21.4476	36.9459	15.4983
	DLGAP4	Divided	Ranked	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]	Low confidence	197.779	211.983	1.07182

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.