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

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.