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	Value Type	Network Comparison Type	Interaction Map	red	Filtered	green	network_comparison

Results: HTML CSV LaTeX

Showing element 575 to 624 of 33156 in total

Network Comparison Type  : Divided
Filtered  : 1

Rank	description	Hugo	Value Type	Interaction Map	red	green	network_comparison
72	solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983]	SLC7A6	Measured	Low confidence	6991.78	7848.45	1.12253
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	PPP2R2D		High confidence	4556.79	2945.28	1.54715
73	carboxypeptidase n 83 kda chain (carboxypeptidase n regulatory subunit) (fragment). [swissprot;acc:p22792]	CPN2	Squared	Low confidence	63279.6	51013.1	1.24046
	eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588]	EIF4B	Measured		6991.78	7848.45	1.12253
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	JPH3	Ranked	High confidence	288	362	1.25694
	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	Squared		219048	129762	1.68808
	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	NEUROD1	Rooted		27.9136	37.2872	1.33581
	rad50-interacting protein 1. [refseq;acc:nm_021930]	RINT1		Low confidence	64.6594	71.0277	1.09849
	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	Measured	High confidence	4556.83	2945.38	1.54711
	set and mynd domain containing protein 1. [sptrembl;acc:q8nb12]	SMYD1	Ranked	Low confidence	230.944	209.149	1.10421
74	b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251]	SLC7A9	Measured		6991.78	7848.45	1.12253
	diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910]	DGKH	Rooted		62.2472	68.3765	1.09847
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	JPH2	Ranked	High confidence	288	362	1.25694
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	NEUROD4	Rooted		27.9136	37.2872	1.33581
	platelet glycoprotein v precursor (gpv) (cd42d). [swissprot;acc:p40197]	GP5	Squared	Low confidence	63279.9	51013.3	1.24046
	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]	AHCYL1	Ranked		195.817	215.516	1.1006
	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	High confidence	4556.99	2945.8	1.54694
	trophinin. [swissprot;acc:q12816]	TRO	Squared		219048	129762	1.68808
75	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	BRAF		Low confidence	63087.3	50932.2	1.23865
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	CHD5	Rooted	High confidence	27.9136	37.2872	1.33581
	diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760]	DGKD		Low confidence	62.2472	68.3765	1.09847
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	MYO5B	Squared	High confidence	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
	nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323]	GBAS	Ranked	Low confidence	249.709	226.944	1.10031
	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	SEPT7	Measured		11616	12942.3	1.11418
	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	Ranked	High confidence	288	362	1.25694
76	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	Rooted		27.9136	37.2872	1.33581
	db83 protein. [swissprot;acc:p57088]	TMEM33	Ranked		288	362	1.25694
	dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5]	XKR7	Rooted	Low confidence	75.1927	82.5511	1.09786
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	MYO5C	Squared	High confidence	110342	184298	1.67024
	nipsnap1 protein. [swissprot;acc:q9bpw8]	NIPSNAP1	Ranked	Low confidence	249.584	226.86	1.10017
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	PANK3	Squared		52172	64605	1.23831
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	PPP1R14A	Measured		5334.13	5933.4	1.11235
	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		High confidence	4599.26	3058.57	1.50373
77	amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817]	SLC7A13	Rooted	Low confidence	68.7629	75.4877	1.0978
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	MFAP4	Measured		5334.13	5933.4	1.11235
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	no value	Squared	High confidence	110342	184298	1.67024
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	PANK2		Low confidence	52168.6	64594.5	1.23819
	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]	no value	Ranked		195.851	215.424	1.09994
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	UNC84A	Rooted	High confidence	39.9725	52.9973	1.32584
	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	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
78	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	1.67008
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	ATF3	Measured		4800.81	7132.71	1.48573
	malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298]	LENG4	Ranked	Low confidence	211	231.635	1.0978
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	PANK1	Squared		52120.9	64447.1	1.23649
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	PPP1R14D	Measured		5334.13	5933.4	1.11235
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	PPP2R2D	Rooted	High confidence	63.7477	48.1589	1.3237
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	CACNG8	Ranked		254.693	202.668	1.2567
	y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01]	SLC7A7	Rooted	Low confidence	68.7629	75.4877	1.0978

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.