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

Results: HTML CSV LaTeX

Showing element 575 to 624 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Hugo	Network Comparison Type	Value Type	red	green	network_comparison
72	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	KCNIP4	Subtracted	Ranked	265.639	319.546	53.907
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	PPP2R2D	Divided	Measured	4556.79	2945.28	1.54715
73	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	DTX1	Subtracted	Rooted	27.7078	44.017	16.3092
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	JPH3	Divided	Ranked	288	362	1.25694
	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	KCNIP2	Subtracted		265.632	319.531	53.899
	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]	MAGED2	Divided	Squared	219048	129762	1.68808
	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	NEUROD1		Rooted	27.9136	37.2872	1.33581
	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]	PPP1R8	Subtracted	Squared	148058	99628.4	48429.6
	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]	PPP2R2B	Divided	Measured	4556.83	2945.38	1.54711
	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	PPP1CC	Subtracted		22268.8	18560.4	3708.4
74	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	ARAF		Squared	117858	70570.1	47287.9
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	no value		Measured	20446.1	24136.4	3690.3
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	JPH2	Divided	Ranked	288	362	1.25694
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	NEUROD4		Rooted	27.9136	37.2872	1.33581
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	PPP2R2C		Measured	4556.99	2945.8	1.54694
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	PPP2R1A	Subtracted	Ranked	189.07	242.453	53.383
	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]	PBK		Rooted	27.7254	44.0299	16.3045
	trophinin. [swissprot;acc:q12816]	TRO	Divided	Squared	219048	129762	1.68808
75	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	CHD5		Rooted	27.9136	37.2872	1.33581
	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	HOXB4	Subtracted	Measured	20446.1	24136.4	3690.3
	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	KHDRBS3		Rooted	27.7254	44.0299	16.3045
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	MYO5B	Divided	Squared	110342	184298	1.67024
	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]	NDUFS4		Measured	1920.75	2907.43	1.5137
	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	RAF1	Subtracted	Squared	117850	70566.8	47283.2
	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]	SMPD2	Divided	Ranked	288	362	1.25694
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	CACNG8	Subtracted		254.693	202.668	52.025
76	cyclin g1 (cyclin g). [swissprot;acc:p51959]	CCNG1		Squared	117718	70505.8	47212.2
	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]	CDK2AP1	Divided	Rooted	27.9136	37.2872	1.33581
	db83 protein. [swissprot;acc:p57088]	TMEM33		Ranked	288	362	1.25694
	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	HOXC5	Subtracted	Measured	20446.1	24136.4	3690.3
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	KHDRBS1		Rooted	27.7254	44.0299	16.3045
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	MYO5C	Divided	Squared	110342	184298	1.67024
	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		Measured	4599.26	3058.57	1.50373
	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	CACNG3	Subtracted	Ranked	254.693	202.668	52.025
77	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	no value		Measured	20446.1	24136.4	3690.3
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	KHDRBS2		Rooted	27.7254	44.0299	16.3045
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	no value	Divided	Squared	110342	184298	1.67024
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	UNC84A		Rooted	39.9725	52.9973	1.32584
	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]	PPP2R5E	Subtracted	Squared	117718	70505.9	47212.1
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	PPP2R1A	Divided	Measured	4612.39	3093.6	1.49095
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	CACNG2		Ranked	254.692	202.668	1.2567
			Subtracted				52.024
78	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	ARAF	Divided	Squared	117858	70570.1	1.67008
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	ATF3		Measured	4800.81	7132.71	1.48573
	cyclin g2. [swissprot;acc:q16589]	CCNG2	Subtracted	Squared	117718	70505.9	47212.1
	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	HOXD4		Measured	20446.1	24136.4	3690.3
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	no value		Rooted	177.987	194.29	16.303
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	PPP2R2D	Divided		63.7477	48.1589	1.3237
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	CACNG4	Subtracted	Ranked	254.691	202.668	52.023
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	CACNG8	Divided		254.693		1.2567

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.