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

Results: HTML CSV LaTeX

Showing element 980 to 1029 of 16578 in total

Value Type  : Ranked
Filtered  : 1

Rank	Hugo	description	Network Comparison Type	Interaction Map	red	network_comparison	green
245	SNRPD3	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Divided	High confidence	226.109	1.11751	202.333
246	no value	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Subtracted		243.583	23.945	267.528
	EIF4G3	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Divided		237.312	1.11748	212.363
	HOXA5	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]		Low confidence	162.755	1.04682	155.476
	OSR1	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Subtracted		217.69	9.269	208.421
247	no value	60s ribosomal protein l12. [swissprot;acc:p30050]		High confidence	243.583	23.944	267.527
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	Low confidence	162.755	1.04682	155.476
		rna-binding protein. [refseq;acc:nm_019027]		High confidence	237.302	1.11719	212.41
	PHKG1	phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform (ec 2.7.1.38) (phosphorylase kinase gamma subunit 1). [swissprot;acc:q16816]	Subtracted	Low confidence	217.957	9.252	227.209
248	no value	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	Divided	High confidence	237.302	1.11719	212.41
		dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Subtracted		243.583	23.944	267.527
	HSD17B14	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Divided	Low confidence	162.755	1.04682	155.476
	TFCP2L1	lbp-9. [refseq;acc:nm_014553]	Subtracted		219.758	9.249	210.509
249	DUOX1	dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434]	Divided		210.487	1.0468	201.076
	SNRPD3	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Subtracted	High confidence	226.109	23.776	202.333
	SYNCRIP	ns1-associated protein 1. [refseq;acc:nm_006372]	Divided		237.302	1.11719	212.41
	TFCP2	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Subtracted	Low confidence	219.749	9.246	210.503
250	AMY1C	alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745]			219.742	9.244	210.498
	DGAT1	diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907]	Divided		210.443	1.04671	201.051
	HNRNPR	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]		High confidence	237.302	1.11719	212.41
	PLDN	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Subtracted		210.693	23.743	186.95
251	NOX5	nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505]	Divided	Low confidence	210.415	1.04666	201.035
	RPS20	40s ribosomal protein s20. [swissprot;acc:p17075]	Subtracted	High confidence	243.5	23.71	267.21
	SLC15A1	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	Divided		186.172	1.11707	166.661
	UBP1	upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517]	Subtracted	Low confidence	219.722	9.238	210.484
252	CYBB	cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839]	Divided		210.414	1.04665	201.035
	EIF4G1	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]		High confidence	237.292	1.11689	212.457
	MXD1	mad protein (max dimerizer). [swissprot;acc:q05195]	Subtracted		228	23.667	204.333
	SNRPB2	u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579]		Low confidence	202.654	9.124	193.53
253	CDC73	parafibromin. [refseq;acc:nm_024529]			214.015	9.099	204.916
	MXD1	mad protein (max dimerizer). [swissprot;acc:q05195]	Divided	High confidence	228	1.11583	204.333
	NFYB	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	Subtracted		251.679	23.642	228.037
	NOX4	nadph oxidase 4. [refseq;acc:nm_016931]	Divided	Low confidence	210.413	1.04665	201.035
254	ATP2C2	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Subtracted		218.785	9.022	209.763
	MXI1	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]		High confidence	227.999	23.642	204.357
	NOX3	nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718]	Divided	Low confidence	210.414	1.04665	201.035
	STT3B	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]		High confidence	200.691	1.11569	179.88
255	MXD4	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Subtracted		227.999	23.633	204.366
	NOX1	nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8]	Divided	Low confidence	210.413	1.04665	201.035
	NUBP2	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Subtracted		200.699	9.021	191.678
	STT3A	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Divided	High confidence	200.691	1.11569	179.88
256	MXI1	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]			227.999		204.357
	RAB24	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Subtracted			23.629	204.37
	SOAT2	sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908]		Low confidence	208.469	9.014	199.455
	STT3A	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Divided		199.376	1.04648	190.521
257	CMPK	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	Subtracted	High confidence	242.14	23.557	265.697
	DDOST	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	Divided		200.691	1.11569	179.88
	JAG2	jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219]	Subtracted	Low confidence	218.715	9.005	209.71
	TPM3	tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753]	Divided		201.316	1.04632	192.404
258	AK3	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	Subtracted	High confidence	242.14	23.557	265.697

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.