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.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 2013 to 2062 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
252	mad protein (max dimerizer). [swissprot;acc:q05195]	Ranked	Subtracted	228	204.333	23.667
	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]	Rooted	Divided	51.6736	58.4422	1.13099
	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148]	Squared		69165	52991.7	1.3052
	sedlin. [swissprot;acc:o14582]	Rooted	Subtracted	116.061	125.434	9.373
253	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]	Squared	Divided	69165	52991.7	1.3052
	endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759]	Measured	Subtracted	9642.22	10986.4	1344.18
	glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807]	Squared		39478.8	48419	8940.2
	mad protein (max dimerizer). [swissprot;acc:q05195]	Ranked	Divided	228	204.333	1.11583
	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	228.037	23.642
	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]	Measured	Divided	6417.18	7859.59	1.22477
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Rooted		53.5956	60.465	1.12817
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]		Subtracted	116.061	125.434	9.373
254	bet3 homolog. [swissprot;acc:o43617]
	glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840]	Measured		9634.98	10976.2	1341.22
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	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]	Measured	Divided	6417.18	7859.6	1.22477
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Rooted		53.607	60.4452	1.12756
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	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]	Squared	Subtracted	59338.5	68268.3	8929.8
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]		Divided	69165	52991.7	1.3052
255	c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]			69123.3	52967	1.30503
	endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759]		Subtracted	39472	48393.1	8921.1
	mad protein (max dimerizer). [swissprot;acc:q05195]	Measured		4455.95	5774.03	1318.08
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Ranked		227.999	204.366	23.633
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]		Divided	200.691	179.88	1.11569
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	Rooted	Subtracted	132.156	122.835	9.321
	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]	Measured	Divided	6417.18	7859.6	1.22477
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Rooted		62.9007	70.8854	1.12694
256	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]			48.0045	54.0843	1.12665
	exocyst complex component sec5. [swissprot;acc:q96kp1]		Subtracted	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]	Squared	Divided	15465.1	20151	1.303
	glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840]		Subtracted	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]	Measured	Divided	6417.19	7859.51	1.22476
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Ranked	Subtracted	227.999	204.37	23.629
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Measured		4456.67	5773.77	1317.1
		Ranked	Divided	227.999	204.357	1.11569
257	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Rooted		51.6125	45.8409	1.12591
	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	Measured		6417.31	7858.12	1.22452
	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	Rooted	Subtracted	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]	Ranked	Divided	200.691	179.88	1.11569
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Squared		15482.3	20162.4	1.30229
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Measured	Subtracted	4456.93	5773.67	1316.74
	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	Squared		33526	42390.2	8864.2
	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	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]
	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	Measured	Divided	6417.33	7857.93	1.22449
	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	Squared		76438	58889.7	1.29799
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Measured	Subtracted	4457.06	5773.63	1316.57
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Ranked	Divided	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]	Squared	Subtracted	33522.8	42384.8	8862

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
- 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.