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	Filtered	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 462 to 511 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Hugo	Value Type	red	network_comparison	green
116	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	GNB3	Ranked	268.565	1.24545	334.483
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	MYH13	Squared	19321	1.54043	12542.6
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	PANK1	Measured	21185	1.34491	28492
117	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	CPSF3	Squared	211446	1.53866	137422
	neuralized-like. [refseq;acc:nm_004210]	NEURL	Ranked	332.326	1.24491	266.948
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	PANK2	Measured	21185	1.34491	28492
	transcription factor jun-b. [swissprot;acc:p17275]	JUNB	Rooted	63.4173	1.25409	79.5311
118	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	HOMER2		50.3065	1.2519	62.9788
	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]	NDUFA12	Ranked	284.753	1.24382	228.934
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	PANK3	Measured	21185	1.34491	28492
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	PAPOLA	Squared	210445	1.53858	136779
119	exocyst complex component sec5. [swissprot;acc:q96kp1]	EXOC2		210335	1.53848	136716
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	SLC25A43	Measured	21185	1.34491	28492
	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	Ranked	318.982	1.23157	259.004
	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	COQ7	Rooted	50.3247	1.25166	62.9892
120	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	HMG20B	Measured	5136.78	1.34247	6895.98
	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	HOMER1	Rooted	50.3333	1.25154	62.9942
	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	PAPOLG	Squared	210199	1.53836	136638
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	KCND2	Ranked	269.278	1.21699	327.709
121	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	CTH		269.254	1.2169	327.655
	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	HOMER3	Rooted	50.339	1.25147	62.9975
	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	PPP1CC	Squared	199594	1.53509	130021
	transcription factor jun-b. [swissprot;acc:p17275]	JUNB	Measured	5579.18	1.3422	7488.4
122	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	CSTF3	Squared	201896	1.53061	131906
	high-mobility group 20a. [refseq;acc:nm_018200]	HMG20A	Measured	5140.14	1.34112	6893.53
	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	KCND3	Ranked	269.248	1.21688	327.642
	transcription factor jun-d. [swissprot;acc:p17535]	JUND	Rooted	63.636	1.25122	79.6225
123	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	ATG4A	Measured	24260.3	1.33503	18172.1
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	TIA1	Rooted	54.6527	1.24375	67.9743
	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	KCND1	Ranked	269.23	1.21681	327.601
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	PPP1R2	Squared	192904	1.52896	126167
124	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	HMG20B	Ranked	208.52	1.21519	171.595
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	MAP1LC3B	Measured	24255.7	1.33501	18168.9
	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	TIAL1	Rooted	54.6625	1.24304	67.9477
	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	PPP1R2P9	Squared	192779	1.52884	126095
125	high-mobility group 20a. [refseq;acc:nm_018200]	HMG20A	Ranked	208.588	1.21429	171.778
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	MAP1LC3A	Measured	24255.7	1.33501	18168.9
	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	RRS1	Squared	189976	1.52616	124480
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	SNRPD1	Rooted	54.8203	1.23921	67.934
126	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	STAMBPL1	Ranked	94	1.21277	114
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	ATG4B	Measured	24250	1.33499	18164.9
	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	HMG20B	Rooted	60.9342	1.23311	75.1387
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	PPP1CA	Squared	189976	1.52616	124480
127	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	no value		88432.6	1.51365	58423.3
	high-mobility group 20a. [refseq;acc:nm_018200]	HMG20A	Rooted	60.9353	1.23236	75.094
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	CHMP2A	Ranked	94	1.21277	114
	transcription factor jun-d. [swissprot;acc:p17535]	JUND	Measured	5638.2	1.33436	7523.39
128	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	STAMBP	Ranked	94	1.21277	114
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	LUC7L2	Measured	4355.61	1.3341	5810.82
	pnas-18. [sptrembl;acc:q9bzu3]	no value	Squared	87787.3	1.50952	58155.8

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.