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 Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 2630 to 2679 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1315	xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [source:refseq;acc:nm_020385]	Subtracted	6123.75	6597.71	473.96	
1316	f-actin capping protein alpha-2 subunit (capz alpha-2). [source:swissprot;acc:p47755]	Subtracted	6339.08	6812.45	473.37	
1316	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [source:swissprot;acc:q9y466]	Divided	6105.93	6599.41	1.08082	
1317	orphan nuclear receptor tr2. [source:swissprot;acc:p13056]	Divided	6105.69	6599.06	1.0808	
1317	p10-binding protein. [source:refseq;acc:nm_024491]	Subtracted	5594.18	6067.49	473.31	
1318	apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [source:refseq;acc:nm_014481]	Subtracted	5546.5	6019.57	473.07	
1318	serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [source:swissprot;acc:q96py6]	Divided	5961.97	6443.07	1.08069	
1319	epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [source:refseq;acc:nm_139204]	Subtracted	5685.38	6157.7	472.32	
1319	serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [source:swissprot;acc:p51956]	Divided	5961.97	6443.07	1.08069	
1320	glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [source:swissprot;acc:p04406]	Divided	5961.97	6443.07	1.08069	
1320	serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [source:swissprot;acc:p34897]	Subtracted	5449.48	5921.77	472.29	
1321	epidermal growth factor receptor kinase substrate eps8. [source:swissprot;acc:q12929]	Subtracted	5685.34	6157.53	472.19	
1321	suppressor of var1, 3-like 1. [source:refseq;acc:nm_003171]	Divided	6439.79	6959.21	1.08066	
1322	bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [source:swissprot;acc:q99933]	Divided	6439.79	6959.21	1.08066	
1322	similar to trna synthetase class ii. [source:refseq;acc:nm_152268]	Subtracted	5439.56	5911.24	471.68	
1323	epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [source:refseq;acc:nm_022772]	Subtracted	5685.08	6156.48	471.4	
1323	glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [source:swissprot;acc:p49840]	Divided	6439.79	6959.21	1.08066	
1324	glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [source:swissprot;acc:p49841]	Divided	6439.79	6959.21	1.08066	
1324	neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [source:refseq;acc:nm_005863]	Subtracted	4086.6	4557.68	471.08	
1325	rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [source:refseq;acc:nm_019555]	Subtracted	4086.6	4557.68	471.08	
1325	serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [source:swissprot;acc:q08209]	Divided	5656.79	6112.02	1.08047	
1326	down-regulated in metastasis. [source:refseq;acc:nm_014503]	Subtracted	4086.6	4557.68	471.08	
1326	mitochondrial gtp binding protein isoform v. [source:refseq;acc:nm_032620]	Divided	6222.8	6723.54	1.08047	
1327	alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [source:swissprot;acc:p42024]	Subtracted	5322.74	5793.15	470.41	
1327	p protein (melanocyte-specific transporter protein). [source:swissprot;acc:q04671]	Divided	5656.8	6111.9	1.08045	
1328	beta-centractin (actin-related protein 1b) (arp1b). [source:swissprot;acc:p42025]	Subtracted	5322.74	5793.15	470.41	
1328	serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [source:swissprot;acc:p16299]	Divided	5656.81	6111.84	1.08044	
1329	serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [source:swissprot;acc:p48454]	Divided	5656.82	6111.8	1.08043	
1329	son of sevenless protein homolog 2 (sos-2). [source:swissprot;acc:q07890]	Subtracted	7497.96	7967.09	469.13	
1330	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [source:swissprot;acc:p41252]	Divided	5779.83	6244.56	1.08041	
1330	upf0202 protein kiaa1709. [source:swissprot;acc:q9h0a0]	Subtracted	3996.81	4465.61	468.8	
1331	glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [source:swissprot;acc:p43304]	Subtracted	6089.43	6558.02	468.59	
1331	transaldolase (ec 2.2.1.2). [source:swissprot;acc:p37837]	Divided	5799.29	6265.2	1.08034	
1332	my016 protein. [source:sptrembl;acc:q9h3k6]	Divided	4775.25	5158.86	1.08033	
1332	n-acetyltransferase 5 (ec 2.3.1.-). [source:swissprot;acc:q9y6d2]	Subtracted	5315.76	5782.63	466.87	
1333	abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [source:refseq;acc:nm_005759]	Divided	5803.95	6269.44	1.0802	
1333	alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [source:swissprot;acc:p35609]	Subtracted	5887.82	6354.58	466.76	
1334	bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [source:swissprot;acc:p07814]	Subtracted	5420.87	5887.53	466.66	
1334	spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [source:refseq;acc:nm_005470]	Divided	5804.75	6270.15	1.08018	
1335	coatomer beta subunit (beta-coat protein) (beta-cop). [source:swissprot;acc:p53618]	Divided	10430.3	9656.4	1.08014	
1335	dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [source:swissprot;acc:q9y463]	Subtracted	5887.86	6354.51	466.65	
1336	dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [source:swissprot;acc:q13627]	Subtracted	5887.86	6354.5	466.64	
1336	g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [source:swissprot;acc:p15170]	Divided	6140.18	6632.24	1.08014	
1337	elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [source:refseq;acc:nm_019040]	Subtracted	5887.86	6354.5	466.64	
1337	gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [source:swissprot;acc:p30793]	Divided	4935.58	5329.93	1.0799	
1338	alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [source:swissprot;acc:p12814]	Subtracted	5887.88	6354.47	466.59	
1338	megf6 (fragment). [source:sptrembl;acc:o75095]	Divided	5980.41	6457.51	1.07978	
1339	6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [source:swissprot;acc:p52209]	Divided	5988.06	6464.94	1.07964	
1339	alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [source:swissprot;acc:o43707]	Subtracted	5887.89	6354.45	466.56	
1340	proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [source:swissprot;acc:p28070]	Divided	5979.07	6453.53	1.07935	

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/