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

Results: HTML CSV LaTeX

Showing element 2025 to 2074 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	Hugo	Value Type	red	green	network_comparison
254	bet3 homolog. [swissprot;acc:o43617]	Subtracted	TRAPPC3	Rooted	116.061	125.434	9.373
	glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840]		GYS2	Measured	9634.98	10976.2	1341.22
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]		MXI1	Ranked	227.999	204.357	23.642
	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]	Divided	FYN	Measured	6417.18	7859.6	1.22477
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]		SRP9	Rooted	53.607	60.4452	1.12756
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]		STT3B	Ranked	200.691	179.88	1.11569
	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	Subtracted	ESRRB	Squared	59338.5	68268.3	8929.8
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	Divided	SNAI2		69165	52991.7	1.3052
255	c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]		CTBP1		69123.3	52967	1.30503
	endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759]	Subtracted	no value		39472	48393.1	8921.1
	mad protein (max dimerizer). [swissprot;acc:q05195]		MXD1	Measured	4455.95	5774.03	1318.08
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]		MXD4	Ranked	227.999	204.366	23.633
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Divided	STT3A		200.691	179.88	1.11569
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	Subtracted	PAPOLA	Rooted	132.156	122.835	9.321
	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]	Divided	FGR	Measured	6417.18	7859.6	1.22477
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]		RRM2	Rooted	62.9007	70.8854	1.12694
256	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]		CEBPZ		48.0045	54.0843	1.12665
	exocyst complex component sec5. [swissprot;acc:q96kp1]	Subtracted	EXOC2		132.114	122.802	9.312
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Divided	no value	Squared	15465.1	20151	1.303
	glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840]	Subtracted	GYS2		39463.9	48362.1	8898.2
	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791]	Divided	GRAP2	Measured	6417.19	7859.51	1.22476
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Subtracted	RAB24	Ranked	227.999	204.37	23.629
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Divided	MXI1			204.357	1.11569
		Subtracted		Measured	4456.67	5773.77	1317.1
257	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Divided	COMP	Rooted	51.6125	45.8409	1.12591
	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]		CUTL1	Measured	6417.31	7858.12	1.22452
	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	Subtracted	CPSF3	Rooted	132.467	123.158	9.309
	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	DDOST	Ranked	200.691	179.88	1.11569
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]		no value	Squared	15482.3	20162.4	1.30229
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Subtracted	MXD4	Measured	4456.93	5773.67	1316.74
	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]		NME2P1	Squared	33526	42390.2	8864.2
	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]		CMPK	Ranked	242.14	265.697	23.557
258	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]		AK3
	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	Divided	CUTL2	Measured	6417.33	7857.93	1.22449
	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]		HIP1	Squared	76438	58889.7	1.29799
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Subtracted	RAB24	Measured	4457.06	5773.63	1316.57
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Divided	MXD4	Ranked	227.999	204.366	1.11564
	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	NME2	Squared	33522.8	42384.8	8862
	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]		PAPOLG	Rooted	132.063	122.761	9.302
	thrombospondin 3 precursor. [swissprot;acc:p49746]	Divided	THBS3		51.6132	45.8422	1.12589
259	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Subtracted	no value	Ranked	242.14	265.696	23.556
	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	COL4A3BP	Squared	76360.8	58841.7	1.29773
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]		RAB24	Ranked	227.999	204.37	1.11562
	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]		WASL	Measured	6417.81	7852.52	1.22355
	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]	Subtracted	no value	Squared	33514.4	42370.8	8856.4
	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]		SEPT4	Rooted	107.961	117.197	9.236
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]		SNRPD3	Measured	4569.48	5885.79	1316.31
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Divided	TFIP11	Rooted	58.2964	65.5926	1.12516
260	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]		HS3ST6	Ranked	219.421	196.978	1.11394
	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	Subtracted	CTPS2	Measured	12515.4	11221.1	1294.3

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.