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

Results: HTML CSV LaTeX

Showing element 61324 to 61373 of 66312 in total

Network Comparison Type  : Subtracted
Interaction Map  : Low confidence
Filtered  : 1

Rank	Value Type	description	Hugo	network_comparison	red	green
3814	Rooted	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]	no value	2.0508	69.309	71.3598
3815	Measured	adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186]	ADRM1	191.19	7992.23	8183.42
	Ranked	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439]	PMPCB	2.632	201.637	199.005
	Squared	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	CDK6	1292.83	1362.75	69.9153
	Rooted	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]	RPS27L	2.0506	71.5508	73.6014
3816	Measured	ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5]	UCHL5	191.19	7992.23	8183.42
	Ranked	kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9]	KIF13A	2.631	202.207	199.576
	Squared	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	LAMP2	1292.83	1362.75	69.9153
	Rooted	udp glycosyltransferase 2 family, polypeptide a1; udp glucuronosyltransferase 2 family, polypeptide a1. [refseq;acc:nm_006798]	UGT2A1	2.0504	69.3049	71.3553
3817	Measured	myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368]	no value	191.15	7852.19	8043.34
	Ranked	conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746]	COG2	2.631	202.207	199.576
	Squared	sorting nexin 15. [swissprot;acc:q9nrs6]	SNX15	1292	45108.6	43816.6
	Rooted	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	2.0503	72.8219	74.8722
3818	Measured	seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591]	SARS	190.77	8335.62	8526.39
	Ranked	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	no value	2.631	202.207	199.576
	Squared	hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]	HAGH	1291.8	44352.5	43060.7
	Rooted	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	PPP2R2D	2.0502	72.8211	74.8713
3819	Measured	calmodulin-related protein nb-1 (calmodulin-like protein) (clp). [swissprot;acc:p27482]	CALML3	190.39	8047.32	8237.71
	Ranked	rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555]	ARHGEF3	2.63	203.077	200.447
	Squared	uridine kinase-like 1. [swissprot;acc:q9nwz5]	no value	1291.2	45677.6	44386.4
	Rooted	udp-glucuronosyltransferase 1-6 precursor, microsomal (ec 2.4.1.17) (udp-glucuronosyltransferase 1a6) (udpgt) (ugt1*6) (ugt1-06) (ugt1.6) (ugt-1f) (ugt1f) (phenol-metabolizing udp-glucuronosyltransferase). [swissprot;acc:p19224]	UGT1A9	2.0502	69.3074	71.3576
3820	Measured	proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789]	PSMA4	190.28	7968.15	8158.43
	Ranked	mitochondrial 28s ribosomal protein s30 (s30mt) (mrp-s30) (programmed cell death protein 9) (bm047). [swissprot;acc:q9np92]	MRPS30	2.629	201.824	199.195
	Squared	dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750]	MAP2K1	1291	45671.5	44380.5
	Rooted	proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3]	PSMA8	2.0501	72.0377	74.0878
3821	Measured	protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6]	TRIOBP	190.18	7855.01	8045.19
	Ranked	neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863]	NET1	2.628	203.086	200.458
	Squared	sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796]	SORD	1289.4	45879.5	44590.1
	Rooted	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156]	PRKCE	2.0495	72.7096	74.7591
3822	Measured	opsin 4 (melanopsin). [swissprot;acc:q9uhm6]	OPN4	190.17	7662.23	7852.4
	Ranked	cellular nucleic acid binding protein (cnbp). [swissprot;acc:p20694]	CNBP	2.628	205.058	202.43
	Squared	diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910]	DGKH	1289.1	36838.1	35549
	Rooted	succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912]	SDHB	2.0486	73.0014	75.05
3823	Measured	hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]	HECTD1	190.17	7662.23	7852.4
	Ranked	60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48]	MRPL34	2.623	204.301	201.678
	Squared	diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760]	DGKD	1289.1	36838.1	35549
	Rooted	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	no value	2.0485	70.8024	72.8509
3824	Measured	rho interacting protein 3. [refseq;acc:nm_015134]		190.16	7855.02	8045.18
	Ranked	orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736]	NR4A1	2.621	197.845	195.224
	Squared	similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5]	KSR1	1288.6	45674.3	44385.7
	Rooted	transcription factor e2-alpha (immunoglobulin enhancer binding factor e12/e47) (transcription factor-3) (tcf-3) (immunoglobulin transcription factor-1) (transcription factor itf-1) (kappa-e2-binding factor). [swissprot;acc:p15923]	TCF3	2.0471	70.8003	72.8474
3825	Measured	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546]	GABPA	190.03	7827.63	8017.66
	Ranked	nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570]	NR4A3	2.62	197.848	195.228
	Squared	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]	COPZ1	1287.6	45652.3	44364.7
	Rooted	homeobox protein engrailed-1 (hu-en-1). [swissprot;acc:q05925]	EN1	2.0469	73.1408	75.1877
3826	Measured	ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545]	no value	190.03	7827.63	8017.66
	Ranked	rcd1 required for cell differentiation1 homolog; protein involved in sexual development; rcd1 (required for cell differentiation, s.pombe) homolog 1. [refseq;acc:nm_005444]	RQCD1	2.617	200.479	197.862
	Squared	dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098]	POLG	1287.5	45769.9	44482.4
	Rooted	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	2.0467	72.8397	74.8864
3827	Measured	arl-6 interacting protein-1 (aip-1). [swissprot;acc:q15041]	ARL6IP1	189.88	8192.6	8382.48

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.