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

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 3364 to 3413 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
841	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]	Rooted	65.0565	69.1533	1.06297
842	jm1 protein. [refseq;acc:nm_014008]	Ranked	219.762	210.806	1.04248
	loh1cr12. [refseq;acc:nm_058169]	Measured	5195.48	5741.63	1.10512
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Squared	31100.1	36086.4	1.16033
	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]	Rooted	65.0565	69.1533	1.06297
843	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690]	Squared	31100.2	36086.5	1.16033
	numb-like protein (numb-r). [swissprot;acc:q9y6r0]	Rooted	65.0565	69.1533	1.06297
	trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102]	Ranked	218.521	227.796	1.04244
	unr protein. [swissprot;acc:o75534]	Measured	5195.48	5741.63	1.10512
844	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	Ranked	178.033	170.82	1.04223
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Squared	31100.2	36086.5	1.16033
	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	Measured	6276.97	6934.8	1.1048
	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]	Rooted	65.0565	69.1533	1.06297
845	dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4]	Measured	6276.97	6934.8	1.1048
	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2]	Squared	31100.1	36086.4	1.16033
	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	Ranked	228.599	219.399	1.04193
	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]	Rooted	65.0565	69.1533	1.06297
846	biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747]	Measured	5607.43	6194.98	1.10478
	keratin associated protein 4.4. [refseq;acc:nm_032524]	Squared	31100.2	36086.5	1.16033
	methyltransferase like 2. [refseq;acc:nm_018396]	Ranked	147.211	153.371	1.04184
	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]	Rooted	65.0565	69.1533	1.06297
847	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Squared	31100.1	36086.4	1.16033
	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]	Ranked	147.211	153.371	1.04184
	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639]	Measured	6776.85	7485.55	1.10458
	wd-repeat protein bing4. [swissprot;acc:o15213]	Rooted	51.7527	55.0117	1.06297
848	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]	Ranked	147.211	153.371	1.04184
	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059]	Squared	31100.1	36086.4	1.16033
	protein bap28. [swissprot;acc:q9h583]	Rooted	51.1817	54.4034	1.06295
	wd-repeat protein bing4. [swissprot;acc:o15213]	Measured	4066.56	4491.65	1.10453
849	dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531]		6194.15	6839.37	1.10417
	integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418]	Squared	31100.1	36086.4	1.16033
	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	Ranked	147.211	153.371	1.04184
	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	Rooted	124.41	117.043	1.06294
850	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]	Ranked	107.842	112.329	1.04161
	propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166]	Measured	6194.15	6839.37	1.10417
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Rooted	124.41	117.043	1.06294
	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4]	Squared	31100.1	36086.4	1.16033
851	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138]	Measured	4307.12	4755.03	1.10399
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Rooted	65.1512	69.252	1.06294
	ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404]	Squared	31100.1	36086.4	1.16033
	trs85 homolog. [swissprot;acc:q9y2l5]	Ranked	107.842	112.329	1.04161
852	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]	Measured	4307.12	4755.03	1.10399
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Ranked	193.114	185.412	1.04154
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Rooted	58.5869	62.2732	1.06292
	ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283]	Squared	31100.1	36086.4	1.16033
853	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	Measured	4078.45	4502.32	1.10393
	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86]	Squared	31100.1	36086.4	1.16033
	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	Rooted	64.0287	68.0566	1.06291
	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Ranked	108.289	112.772	1.0414
854	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]

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.