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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2601 to 2650 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1301	electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [source:swissprot;acc:q16134]	Divided	6618.74	7161.67	1.08203	
1301	mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [source:swissprot;acc:o95382]	Subtracted	6079.46	6555.4	475.94	
1302	mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [source:swissprot;acc:q99683]	Subtracted	6079.46	6555.4	475.94	
1302	peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [source:swissprot;acc:q13162]	Divided	6343.26	6862.94	1.08193	
1303	cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [source:refseq;acc:nm_016441]	Divided	6334.15	6852.61	1.08185	
1303	mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [source:swissprot;acc:p28482]	Subtracted	6079.13	6554.85	475.72	
1304	fibulin-1 precursor. [source:swissprot;acc:p23142]	Divided	8550.79	9248.06	1.08154	
1304	testis-specific chromodomain protein y protein 2. [source:swissprot;acc:q9y6f7]	Subtracted	7101.16	7576.87	475.71	
1305	glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [source:swissprot;acc:p47897]	Divided	5500.92	5949.26	1.0815	
1305	testis-specific chromodomain y protein 1. [source:swissprot;acc:q9y6f8]	Subtracted	7101.15	7576.84	475.69	
1306	chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [source:refseq;acc:nm_004824]	Subtracted	7101.15	7576.84	475.69	
1306	spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [source:swissprot;acc:p19623]	Divided	5500.92	5949.26	1.0815	
1307	glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [source:swissprot;acc:p41250]	Divided	5500.92	5949.26	1.0815	
1307	nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [source:swissprot;acc:o96000]	Subtracted	6362.92	6838.6	475.68	
1308	glutamyl trna synthetase. [source:sptrembl;acc:o14563]	Divided	5500.92	5949.26	1.0815	
1308	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [source:swissprot;acc:p25388]	Subtracted	4489.72	4965.35	475.63	
1309	protein ad-016 (protein cgi-116) (x0009). [source:swissprot;acc:q9y3c0]	Divided	6110.09	6607.81	1.08146	
1309	zuotin related factor-1 (m-phase phosphoprotein 11). [source:swissprot;acc:q99543]	Subtracted	4489.72	4965.35	475.63	
1310	casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [source:swissprot;acc:p49674]	Subtracted	5048.33	5523.85	475.52	
1310	mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [source:swissprot;acc:q15750]	Divided	6051.23	6544.17	1.08146	
1311	casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [source:swissprot;acc:p48730]	Subtracted	5054.73	5530.23	475.5	
1311	exocyst complex component sec8. [source:swissprot;acc:q96a65]	Divided	6221.22	6727.77	1.08142	
1312	putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [source:swissprot;acc:o75153]	Subtracted	5464.9	5940.16	475.26	
1312	u2 small nuclear ribonucleoprotein b". [source:swissprot;acc:p08579]	Divided	5675.96	6136.47	1.08113	
1313	60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [source:swissprot;acc:p10809]	Divided	5457.14	5899.85	1.08112	
1313	f-actin capping protein alpha-1 subunit (capz alpha-1). [source:swissprot;acc:p52907]	Subtracted	6340.5	6815.41	474.91	
1314	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]	Subtracted	5979.07	6453.53	474.46	
1314	vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [source:swissprot;acc:q9nrw7]	Divided	5401.39	5838.63	1.08095	
1315	dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [source:swissprot;acc:p54098]	Divided	5685.77	6145.43	1.08084	
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	

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/