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

Results: HTML CSV LaTeX

Showing element 1932 to 1981 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	Network Comparison Type	description	Value Type	red	green	network_comparison
242	DNAJC12	Divided	j domain containing protein 1. [swissprot;acc:q9ukb3]	Ranked	227.357	254.15	1.11785
	KYNU	Subtracted	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	Squared	35991.8	46002.9	10011.1
	MAGED2	Divided	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]	Rooted	137.446	120.823	1.13758
	MAX		max protein. [swissprot;acc:p25912]	Measured	4640.26	5704.87	1.22943
	RAB24	Subtracted	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Rooted	55.65	65.1448	9.4948
243	no value		60s ribosomal protein l23a. [swissprot;acc:p29316]	Ranked	241.884	265.945	24.061
	CHRNA3		neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]	Measured	9649.61	11053.5	1403.89
	DRAP1		dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	Squared	51805.2	41916.4	9888.8
	HOMER2	Divided	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Measured	4246.95	5208.98	1.22652
	PLDN	Subtracted	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Rooted	63.1192	72.584	9.4648
	SNX13	Divided	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	Ranked	227.357	254.15	1.11785
	SPHK2		sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]	Squared	42411.6	55802.1	1.31573
	TRO		trophinin. [swissprot;acc:q12816]	Rooted	137.446	120.823	1.13758
244	no value	Subtracted	scratch; scratch 1. [refseq;acc:nm_031309]	Squared	40388.9	49827.5	9438.6
	COQ7	Divided	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	Measured	4250.14	5211.25	1.22614
	GSTO2		ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	Ranked	227.357	254.15	1.11785
	MYO5B		myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Rooted	146.94	167.046	1.13683
	NCBP2L		dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Squared	14728.8	19330.8	1.31245
	NEUROD2	Subtracted	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Rooted	27.9136	37.2872	9.3736
	RPL5		60s ribosomal protein l5. [swissprot;acc:p46777]	Ranked	241.899	265.924	24.025
	SPHK2		sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]	Measured	9649.61	11053.5	1403.89
245	no value		dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	Squared	40315.7	49716.4	9400.7
			methyltransferase like 2. [refseq;acc:nm_018396]	Measured	13241.4	11864	1377.4
	CHD3		chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Rooted	27.9136	37.2872	9.3736
	GBE1	Divided	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Squared	8875.01	6768.05	1.31131
	HOMER1		homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Measured	4251.65	5212.33	1.22595
	MYO5C		myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Rooted	146.94	167.046	1.13683
	RPL19	Subtracted	60s ribosomal protein l19. [swissprot;acc:p14118]	Ranked	240.73	264.729	23.999
	SNRPD3	Divided	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]		226.109	202.333	1.11751
246	no value		myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Rooted	146.94	167.046	1.13683
		Subtracted	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Ranked	243.583	267.528	23.945
	CDK2AP2		doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Rooted	27.9136	37.2872	9.3736
	DYNLT1		cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]	Measured	13241.4	11864	1377.4
	EIF4G3	Divided	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Ranked	237.312	212.363	1.11748
	HHEX	Subtracted	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014]	Squared	54726.7	45358.5	9368.2
	HOMER3	Divided	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	Measured	4252.66	5213.05	1.22583
	PYGB		glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Squared	8875.01	6768.05	1.31131
247	no value		rna-binding protein. [refseq;acc:nm_019027]	Ranked	237.302	212.41	1.11719
		Subtracted	60s ribosomal protein l12. [swissprot;acc:p30050]		243.583	267.527	23.944
	DDX56	Divided	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Rooted	47.3621	53.8355	1.13668
	FZR1	Subtracted	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]	Measured	13241.4	11864	1377.4
	NEUROD6		neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Rooted	27.9136	37.2872	9.3736
	NME3		nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232]	Squared	33982.3	43159.1	9176.8
	PYGL	Divided	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]		8875.01	6768.05	1.31131
	WAS		wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	Measured	6416.68	7865.15	1.22574
248	no value		apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	Ranked	237.302	212.41	1.11719
		Subtracted	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]		243.583	267.527	23.944
	CRK	Divided	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	Measured	6417.18	7859.6	1.22477
	IDH2	Subtracted	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735]	Squared	37226.9	46400.1	9173.2
	LSM5	Divided	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	Rooted	56.0466	63.4808	1.13264

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.