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	green	network_comparison

Results: HTML CSV LaTeX

Showing element 2051 to 2100 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	Network Comparison Type	Value Type	red	green	network_comparison
257	COMP	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Divided	Rooted	51.6125	45.8409	1.12591
	CPSF3	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	Subtracted		132.467	123.158	9.309
	CUTL1	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	Divided	Measured	6417.31	7858.12	1.22452
	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]		Ranked	200.691	179.88	1.11569
	MXD4	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Subtracted	Measured	4456.93	5773.67	1316.74
	NME2P1	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]		Squared	33526	42390.2	8864.2
258	AK3	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]		Ranked	242.14	265.697	23.557
	CUTL2	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	Divided	Measured	6417.33	7857.93	1.22449
	HIP1	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]		Squared	76438	58889.7	1.29799
	MXD4	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]		Ranked	227.999	204.366	1.11564
	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]	Subtracted	Squared	33522.8	42384.8	8862
	PAPOLG	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]		Rooted	132.063	122.761	9.302
	RAB24	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]		Measured	4457.06	5773.63	1316.57
	THBS3	thrombospondin 3 precursor. [swissprot;acc:p49746]	Divided	Rooted	51.6132	45.8422	1.12589
259	no value	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Subtracted	Ranked	242.14	265.696	23.556
		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	8856.4
	COL4A3BP	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4]	Divided		76360.8	58841.7	1.29773
	RAB24	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]		Ranked	227.999	204.37	1.11562
	SEPT4	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	Subtracted	Rooted	107.961	117.197	9.236
	SNRPD3	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]		Measured	4569.48	5885.79	1316.31
	TFIP11	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Divided	Rooted	58.2964	65.5926	1.12516
	WASL	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]		Measured	6417.81	7852.52	1.22355
260	CTPS2	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	Subtracted		12515.4	11221.1	1294.3
	HIP1R	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	Divided	Squared	76296.4	58801.6	1.29752
	HS3ST6	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]		Ranked	219.421	196.978	1.11394
	MED22	surfeit locus protein 5. [swissprot;acc:q15528]	Subtracted		242.14	265.696	23.556
	SCYE1	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	Divided	Rooted	59.0951	66.4332	1.12417
	SF3B1	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Subtracted		56.7592	65.9889	9.2297
	SH3GL1	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]		Squared	35793	44595.3	8802.3
	SRP9	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Divided	Measured	4244.95	5193.42	1.22343
261	CPA5	carboxypeptidase a5. [refseq;acc:nm_080385]	Subtracted	Squared	53174	44377.4	8796.6
	EIF4G3	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]		Rooted	52.7582	61.9123	9.1541
	HS3ST3A1	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	Divided	Ranked	219.421	196.978	1.11394
	PC	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]		Squared	48127.9	62245.6	1.29334
	RRM2B	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]		Rooted	62.3337	70.0738	1.12417
	SCAPER	zinc finger protein 291. [swissprot;acc:q9by12]	Subtracted	Ranked	242.14	265.696	23.556
	SRP9	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Divided	Measured	4247.36	5192.61	1.22255
	STT3B	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Subtracted		4571.89	5864.86	1292.97
262	no value	rna-binding protein. [refseq;acc:nm_019027]		Rooted	52.7642	61.9019	9.1377
	CHRNA7	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	Divided	Squared	26157.6	20236.2	1.29261
	CPB1	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086]	Subtracted		53174	44377.4	8796.6
	CPSF4	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	Divided	Measured	24896.4	20431.7	1.21852
	HS3ST3B1	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]		Ranked	219.421	196.978	1.11394
	PEX1	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]	Subtracted		242.14	265.696	23.556
	POLI	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	Divided	Rooted	59.4073	66.7002	1.12276
	STT3A	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Subtracted	Measured	4571.89	5864.86	1292.97
263	no value	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]		Rooted	52.7642	61.9019	9.1377
	ADCY6	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	Divided	Squared	26157.6	20236.2	1.29261
	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]	Subtracted	Measured	4571.89	5864.86	1292.97
	HS3ST2	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	Divided	Ranked	219.421	196.978	1.11394

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.