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

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 2701 to 2750 of 33156 in total

Network Comparison Type  : Divided
Filtered  : 1

Rank	Value Type	Hugo	description	Interaction Map	network_comparison	red	green
338	Squared	HIVEP1	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822]	High confidence	1.24789	46785.7	58383.2
		RSPH3	radial spokehead-like 2; radial spoke protein 3. [refseq;acc:nm_031924]	Low confidence	1.07717	48506.5	45031.6
	Rooted	CPA3	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	High confidence	1.108	77.58	70.0181
		RAB24	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Low confidence	1.05195	67.7254	71.2438
339	Measured	HOXC5	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	High confidence	1.18049	20446.1	24136.4
		IDH2	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735]	Low confidence	1.05561	9114.82	9621.71
	Ranked	no value	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	High confidence	1.0983	243.583	267.527
		GGPS1	geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749]	Low confidence	1.03951	209.518	201.554
	Squared	EVI1	ecotropic virus integration 1 site protein. [swissprot;acc:q03112]		1.07658	53275.3	49485.7
		HIVEP2	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]	High confidence	1.24789	46785.7	58383.2
	Rooted	no value	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Low confidence	1.05188	71.5541	75.2665
		CPB2	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	High confidence	1.108	77.5797	70.0179
340	Measured	no value	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		1.18049	20446.1	24136.4
		CLEC3B	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	Low confidence	1.0556	8940.43	9437.54
	Ranked	BET1L	blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526]		1.03939	201.827	194.178
		MYEF2	myelin gene expression factor 2. [refseq;acc:nm_016132]	High confidence	1.09811	235.383	258.476
	Squared	no value	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Low confidence	1.07628	50915	47306.4
		RRM2B	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	High confidence	1.24713	32117	40054
	Rooted	PRPF19	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]		1.10791	58.4926	64.8047
		RABEP1	rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703]	Low confidence	1.05187	71.2599	74.9558
341	Measured	ARHGEF7	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155]		1.05557	7151	7548.35
		HOXD4	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	High confidence	1.18049	20446.1	24136.4
	Ranked	no value	60s ribosomal protein l9. [swissprot;acc:p32969]		1.09805	240.243	263.798
		KCNIP1	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Low confidence	1.03919	214.027	222.415
	Squared	no value	alpha-nac protein. [sptrembl;acc:q9h009]		1.07627	50910.5	47302.9
		RRM1	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	High confidence	1.24673	32056.4	39965.8
	Rooted	BET1L	blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526]	Low confidence	1.05181	72.4676	76.2225
		SSB	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	High confidence	1.10782	51.9812	57.5858
342	Measured	HOXB5	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]		1.18049	20446.1	24136.4
		OGT	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294]	Low confidence	1.05548	7309.92	7715.51
	Ranked	no value	tho complex 3. [refseq;acc:nm_032361]		1.03907	186.383	179.374
		RPS20	40s ribosomal protein s20. [swissprot;acc:p17075]	High confidence	1.09737	243.5	267.21
	Squared	DIRAS1	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	Low confidence	1.07626	50908.3	47301
		HGS	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	High confidence	1.24653	70830.5	56822
	Rooted	CRNKL1	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Low confidence	1.05158	70.4474	74.0813
		EBNA1BP2	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	High confidence	1.10765	49.2715	54.5757
343	Measured	ARHGEF6	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052]	Low confidence	1.05538	7155.19	7551.48
		HOXA5	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	High confidence	1.18049	20446.1	24136.4
	Ranked	KCNIP4	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Low confidence	1.03899	213.982	222.326
		PRMT3	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	High confidence	1.0973	241.625	265.136
	Squared	COG7	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]		1.24653	70830.5	56822
		DIRAS2	di-ras2. [refseq;acc:nm_017594]	Low confidence	1.07626	50908.1	47300.9
	Rooted	no value	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	High confidence	1.10749	50.3169	45.4333
		SNRPD2	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Low confidence	1.05155	71.3123	74.9882
344	Measured	no value	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	High confidence	1.18049	20446.1	24136.4
		CLEC3A	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	Low confidence	1.05528	8926.58	9420
	Ranked	no value	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	High confidence	1.0973	241.625	265.136
		MRPL44	mitochondrial ribosomal protein l44. [refseq;acc:nm_022915]	Low confidence	1.03896	216.283	208.173
	Squared	IDH2	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735]	High confidence	1.24641	37226.9	46400.1
		TM9SF3	transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [swissprot;acc:q9hd45]	Low confidence	1.07596	49200	45726.8

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.