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

Results: HTML CSV LaTeX

Showing element 1258 to 1307 of 12912 in total

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

Rank	Hugo	description	Value Type	red	green	network_comparison
315	MYH1	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Rooted	95.0526	85.3206	1.11406
	PCSK5	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	Squared	71576.8	56326.7	1.27074
	RRS1	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	Measured	21370.8	17896.5	1.19413
316	no value	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	Rooted	95.0526	85.3206	1.11406
	EIF1	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	Ranked	242.694	267.017	1.10022
	PPP1CA	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Measured	21370.8	17896.5	1.19413
	WASL	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	Squared	28918.3	36746	1.27068
317	no value	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Ranked	224.445	204.044	1.09998
	ADIPOR2	adiponectin receptor 2. [refseq;acc:nm_024551]	Measured	3153.1	3762.56	1.19329
	MYH7B	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Rooted	95.0526	85.3206	1.11406
	NME3	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232]	Squared	33982.3	43159.1	1.27005
318	no value	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured	34190.9	40795.8	1.19318
	MRPL3	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	Ranked	242.011	266.18	1.09987
	MYH13	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Rooted	95.0526	85.3206	1.11406
	TOMM20	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388]	Squared	46739.9	59134.5	1.26518
319	NIP7	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	Rooted	49.0663	54.4978	1.1107
	PEX19	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]	Squared	46739.9	59134.5	1.26518
	RPL19	60s ribosomal protein l19. [swissprot;acc:p14118]	Ranked	240.73	264.729	1.09969
	RRAGA	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Measured	20911	24908.5	1.19117
320	no value	40s ribosomal protein s29. [swissprot;acc:p30054]	Rooted	50.2784	45.294	1.11005
	CDH1	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	Ranked	241.892	265.96	1.0995
	EPHX1	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099]	Squared	87971.9	69563.1	1.26463
	RRAGC	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Measured	20911	24908.5	1.19117
321	no value	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Ranked	241.892	265.959	1.09949
		u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Rooted	55.9231	62.0565	1.10968
	NME2P1	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	Squared	33526	42390.2	1.2644
	RRAGB	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Measured	20911	24908.5	1.19117
322	ANLN	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
	DNASE2B	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Ranked	86.7483	78.8995	1.09948
	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Rooted	60.594	67.2244	1.10942
	NME2	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531]	Squared	33522.8	42384.8	1.26436
323	no value	60s ribosomal protein l23a. [swissprot;acc:p29316]	Ranked	241.884	265.945	1.09947
		nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392]	Squared	33514.4	42370.8	1.26426
	LSM4	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	Measured	4620.76	5501.94	1.1907
	PCYT1A	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	Rooted	50.3803	45.4193	1.10923
324	DNASE2B	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Measured	28136.5	33457.6	1.18912
	FLAD1	fad synthetase. [refseq;acc:nm_025207]	Rooted	50.3803	45.4193	1.10923
	HARS2	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	Squared	34527.9	43507.9	1.26008
	RPS23	40s ribosomal protein s23. [swissprot;acc:p39028]	Ranked	243.944	268.195	1.09941
325	no value	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Rooted	50.3803	45.4193	1.10923
	HARS	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	Squared	34506.3	43476	1.25994
	MRPS12	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	Ranked	243.944	268.195	1.09941
	SEPT8	septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]	Measured	16177.9	19235.4	1.18899
326	ANAPC2	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366]	Squared	69124.3	54897.4	1.25915
	DDX24	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	Measured	3432.96	4081.21	1.18883
	LGTN	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]	Rooted	50.3803	45.4193	1.10923
	RPL5	60s ribosomal protein l5. [swissprot;acc:p46777]	Ranked	241.899	265.924	1.09932
327	LUC7L2	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Squared	16424.1	20645.8	1.25704
	PAPSS1	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252]	Rooted	50.3803	45.4193	1.10923
	POLR2A	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	Ranked	243.817	267.962	1.09903

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.