Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

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 Interaction Map Network Comparison Type Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 2058 to 2107 of 14920 in total

Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
258	40s ribosomal protein s28. [source:swissprot;acc:p25112]	Ranked	0	12967.1	14193.6	1.09459	
258	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Rooted	0	21.1334	23.34	1.10441	
258	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	Squared	0	2783.53	3517.26	1.2636	
258	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Measured	1	6417.33	7857.93	1.22449	
258	huntingtin interacting protein 1 (hip-i). [source:swissprot;acc:o00291]	Squared	1	76438	58889.7	1.29799	
258	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Ranked	1	227.999	204.366	1.11564	
258	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	Rooted	1	51.6132	45.8422	1.12589	
259	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [source:swissprot;acc:p08865]	Rooted	0	21.9471	19.8816	1.10389	
259	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Squared	0	3438.01	4339.96	1.26235	
259	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	Measured	0	1295.49	1463.51	1.1297	
259	adenylyl cyclase-associated protein 2 (cap 2). [source:swissprot;acc:p40123]	Ranked	0	10438.3	9549.77	1.09304	
259	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). [source:swissprot;acc:q9y5p4]	Squared	1	76360.8	58841.7	1.29773	
259	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Ranked	1	227.999	204.37	1.11562	
259	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Measured	1	6417.81	7852.52	1.22355	
259	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	Rooted	1	58.2964	65.5926	1.12516	
260	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Ranked	0	12447.6	11392.6	1.0926	
260	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	Ranked	1	219.421	196.978	1.11394	
260	histone h4. [source:swissprot;acc:p02304]	Squared	0	273623	345123	1.26131	
260	huntingtin interacting protein 1 related (hip1-related) (hip 12). [source:swissprot;acc:o75146]	Squared	1	76296.4	58801.6	1.29752	
260	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	Rooted	1	59.0951	66.4332	1.12417	
260	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Rooted	0	22.3157	24.6207	1.10329	
260	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Measured	1	4244.95	5193.42	1.22343	
260	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	Measured	0	1949.36	2202	1.1296	
261	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Ranked	0	12448.9	11393.9	1.09259	
261	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Rooted	0	22.315	24.6198	1.10328	
261	apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	Squared	0	135280	170628	1.2613	
261	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	Measured	0	1295.81	1463.55	1.12945	
261	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	Ranked	1	219.421	196.978	1.11394	
261	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [source:swissprot;acc:p11498]	Squared	1	48127.9	62245.6	1.29334	
261	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Rooted	1	62.3337	70.0738	1.12417	
261	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Measured	1	4247.36	5192.61	1.22255	
262	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Squared	0	2463.89	3102.4	1.25915	
262	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Rooted	0	26.0693	28.761	1.10325	
262	adenylyl cyclase-associated protein 2 (cap 2). [source:swissprot;acc:p40123]	Measured	0	764.479	676.971	1.12926	
262	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [source:refseq;acc:nm_006693]	Measured	1	24896.4	20431.7	1.21852	
262	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	Ranked	1	219.421	196.978	1.11394	
262	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	Squared	1	26157.6	20236.2	1.29261	
262	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	Rooted	1	59.4073	66.7002	1.12276	
262	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [source:refseq;acc:nm_016538]	Ranked	0	3464	3778	1.09065	
263	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	Squared	1	26157.6	20236.2	1.29261	
263	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [source:swissprot;acc:p56559]	Rooted	0	4.79583	4.3589	1.10024	
263	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Ranked	0	13573.3	14801.2	1.09046	
263	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	Ranked	1	219.421	196.978	1.11394	
263	paxillin. [source:swissprot;acc:p49023]	Rooted	1	59.4073	66.7002	1.12276	
263	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Squared	0	2463.98	3102.52	1.25915	
263	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [source:refseq;acc:nm_016538]	Measured	0	1843	1633	1.1286	
263	trs85 homolog. [source:swissprot;acc:q9y2l5]	Measured	1	24896.4	20431.7	1.21852	
264	60s ribosomal protein l12. [source:swissprot;acc:p30050]	Squared	0	3686.65	4639.46	1.25845	
264	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	Squared	1	26157.6	20236.2	1.29261	
264	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [source:swissprot;acc:o43681]	Ranked	0	10037.1	10935.1	1.08947	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/