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

Results: HTML CSV LaTeX

Showing element 1008 to 1057 of 12912 in total

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

Rank	Value Type	description	Hugo	red	green	network_comparison
252	Rooted	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]	NFYB	51.6736	58.4422	1.13099
253	Measured	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]	ABL1	6417.18	7859.59	1.22477
	Ranked	mad protein (max dimerizer). [swissprot;acc:q05195]	MXD1	228	204.333	1.11583
	Squared	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]	BCL6	69165	52991.7	1.3052
	Rooted	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	SRP9	53.5956	60.465	1.12817
254	Measured	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]	FYN	6417.18	7859.6	1.22477
	Ranked	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	STT3B	200.691	179.88	1.11569
	Squared	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	SNAI2	69165	52991.7	1.3052
	Rooted	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	SRP9	53.607	60.4452	1.12756
255	Measured	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]	FGR	6417.18	7859.6	1.22477
	Ranked	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	STT3A	200.691	179.88	1.11569
	Squared	c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]	CTBP1	69123.3	52967	1.30503
	Rooted	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	RRM2	62.9007	70.8854	1.12694
256	Measured	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]	GRAP2	6417.19	7859.51	1.22476
	Ranked	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	MXI1	227.999	204.357	1.11569
	Squared	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	no value	15465.1	20151	1.303
	Rooted	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	CEBPZ	48.0045	54.0843	1.12665
257	Measured	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	CUTL1	6417.31	7858.12	1.22452
	Ranked	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]	DDOST	200.691	179.88	1.11569
	Squared	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	no value	15482.3	20162.4	1.30229
	Rooted	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	COMP	51.6125	45.8409	1.12591
258	Measured	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	CUTL2	6417.33	7857.93	1.22449
	Ranked	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	MXD4	227.999	204.366	1.11564
	Squared	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	HIP1	76438	58889.7	1.29799
	Rooted	thrombospondin 3 precursor. [swissprot;acc:p49746]	THBS3	51.6132	45.8422	1.12589
259	Measured	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	WASL	6417.81	7852.52	1.22355
	Ranked	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	RAB24	227.999	204.37	1.11562
	Squared	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]	COL4A3BP	76360.8	58841.7	1.29773
	Rooted	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	TFIP11	58.2964	65.5926	1.12516
260	Measured	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	SRP9	4244.95	5193.42	1.22343
	Ranked	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	HS3ST6	219.421	196.978	1.11394
	Squared	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	HIP1R	76296.4	58801.6	1.29752
	Rooted	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	SCYE1	59.0951	66.4332	1.12417
261	Measured	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	SRP9	4247.36	5192.61	1.22255
	Ranked	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	HS3ST3A1	219.421	196.978	1.11394
	Squared	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]	PC	48127.9	62245.6	1.29334
	Rooted	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	RRM2B	62.3337	70.0738	1.12417
262	Measured	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]	CPSF4	24896.4	20431.7	1.21852
	Ranked	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	HS3ST3B1	219.421	196.978	1.11394
	Squared	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	CHRNA7	26157.6	20236.2	1.29261
	Rooted	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	POLI	59.4073	66.7002	1.12276
263	Measured	trs85 homolog. [swissprot;acc:q9y2l5]	KIAA1012	24896.4	20431.7	1.21852
	Ranked	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	HS3ST2	219.421	196.978	1.11394
	Squared	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	ADCY6	26157.6	20236.2	1.29261
	Rooted	paxillin. [swissprot;acc:p49023]	PXN	59.4073	66.7002	1.12276
264	Measured	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	COPS3	4987.58	4094.57	1.2181
	Ranked	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	DCPS	219.421	196.978	1.11394
	Squared	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	ADCY5	26157.6	20236.2	1.29261
	Rooted	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	WAS	66.1122	74.1438	1.12148
265	Measured	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	WDR33	24806.9	20369.9	1.21782

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.