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

Results: HTML CSV LaTeX

Showing element 468 to 517 of 12912 in total

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

Rank	Hugo	Value Type	description	red	network_comparison	green
117	PANK2	Measured	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	21185	1.34491	28492
118	HOMER2	Rooted	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	50.3065	1.2519	62.9788
	NDUFA12	Ranked	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]	284.753	1.24382	228.934
	PANK3	Measured	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	21185	1.34491	28492
	PAPOLA	Squared	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	210445	1.53858	136779
119	COQ7	Rooted	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	50.3247	1.25166	62.9892
	EXOC2	Squared	exocyst complex component sec5. [swissprot;acc:q96kp1]	210335	1.53848	136716
	NDUFS4	Ranked	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]	318.982	1.23157	259.004
	SLC25A43	Measured	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	21185	1.34491	28492
120	HMG20B		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]	5136.78	1.34247	6895.98
	HOMER1	Rooted	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	50.3333	1.25154	62.9942
	KCND2	Ranked	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	269.278	1.21699	327.709
	PAPOLG	Squared	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	210199	1.53836	136638
121	CTH	Ranked	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	269.254	1.2169	327.655
	HOMER3	Rooted	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	50.339	1.25147	62.9975
	JUNB	Measured	transcription factor jun-b. [swissprot;acc:p17275]	5579.18	1.3422	7488.4
	PPP1CC	Squared	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	199594	1.53509	130021
122	CSTF3		cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	201896	1.53061	131906
	HMG20A	Measured	high-mobility group 20a. [refseq;acc:nm_018200]	5140.14	1.34112	6893.53
	JUND	Rooted	transcription factor jun-d. [swissprot;acc:p17535]	63.636	1.25122	79.6225
	KCND3	Ranked	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]	269.248	1.21688	327.642
123	ATG4A	Measured	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	24260.3	1.33503	18172.1
	KCND1	Ranked	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	269.23	1.21681	327.601
	PPP1R2	Squared	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	192904	1.52896	126167
	TIA1	Rooted	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	54.6527	1.24375	67.9743
124	HMG20B	Ranked	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]	208.52	1.21519	171.595
	MAP1LC3B	Measured	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	24255.7	1.33501	18168.9
	PPP1R2P9	Squared	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	192779	1.52884	126095
	TIAL1	Rooted	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	54.6625	1.24304	67.9477
125	HMG20A	Ranked	high-mobility group 20a. [refseq;acc:nm_018200]	208.588	1.21429	171.778
	MAP1LC3A	Measured	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	24255.7	1.33501	18168.9
	RRS1	Squared	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	189976	1.52616	124480
	SNRPD1	Rooted	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	54.8203	1.23921	67.934
126	ATG4B	Measured	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	24250	1.33499	18164.9
	HMG20B	Rooted	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]	60.9342	1.23311	75.1387
	PPP1CA	Squared	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	189976	1.52616	124480
	STAMBPL1	Ranked	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	94	1.21277	114
127	no value	Squared	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	88432.6	1.51365	58423.3
	CHMP2A	Ranked	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	94	1.21277	114
	HMG20A	Rooted	high-mobility group 20a. [refseq;acc:nm_018200]	60.9353	1.23236	75.094
	JUND	Measured	transcription factor jun-d. [swissprot;acc:p17535]	5638.2	1.33436	7523.39
128	no value	Squared	pnas-18. [sptrembl;acc:q9bzu3]	87787.3	1.50952	58155.8
	LUC7L2	Measured	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	4355.61	1.3341	5810.82
	STAMBP	Ranked	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	94	1.21277	114
	TARDBP	Rooted	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	48.0515	1.23069	39.0445
129	LUC7L	Measured	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	4358.13	1.33348	5811.49
	NCBP2L	Rooted	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	54.2343	1.23044	66.7323
	PCF11	Squared	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	178263	1.50257	118639
	VPS24	Ranked	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	94	1.21277	114
130	no value	Rooted	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	55.1026	1.22626	67.5701

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.