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 2558 to 2607 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1279	heat shock cognate 71 kda protein. [source:swissprot;acc:p11142]	Divided	6437.99	6969.67	1.08258	
1280	actin, cytoplasmic 2 (gamma-actin). [source:swissprot;acc:p02571]	Subtracted	6036.22	6512.64	476.42	
1280	dehydrodolichyl diphosphate synthase. [source:refseq;acc:nm_024887]	Divided	6350.81	6874.88	1.08252	
1281	dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [source:swissprot;acc:q13561]	Subtracted	5322.16	5798.38	476.22	
1281	orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [source:swissprot;acc:p22736]	Divided	6230.49	6744.5	1.0825	
1282	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	Subtracted	5322.16	5798.38	476.22	
1282	nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [source:swissprot;acc:q92570]	Divided	6230.38	6744.35	1.08249	
1283	adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [source:swissprot;acc:p12235]	Subtracted	5322.16	5798.38	476.22	
1283	orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [source:swissprot;acc:p43354]	Divided	6229.16	6742.79	1.08246	
1284	mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [source:swissprot;acc:p27361]	Subtracted	6079.85	6556.07	476.22	
1284	xenotropic and polytropic retrovirus receptor. [source:refseq;acc:nm_004736]	Divided	6413.32	6941.48	1.08235	
1285	adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [source:swissprot;acc:p05141]	Subtracted	5322.16	5798.38	476.22	
1285	cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [source:swissprot;acc:q96kp4]	Divided	6207.57	6718.7	1.08234	
1286	casein kinase i alpha s-like. [source:refseq;acc:nm_145203]	Subtracted	4906.33	5382.5	476.17	
1286	cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [source:swissprot;acc:q02928]	Divided	5655.85	6120.64	1.08218	
1287	casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [source:swissprot;acc:p48729]	Subtracted	4906.33	5382.5	476.17	
1287	cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:q08477]	Divided	5655.85	6120.64	1.08218	
1288	chromodomain y-like protein 2. [source:refseq;acc:nm_152342]	Subtracted	7101.7	7577.75	476.05	
1288	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	Divided	5655.85	6120.64	1.08218	
1289	likely ortholog of rat cytochrome p450 4x1. [source:refseq;acc:nm_178033]	Divided	5655.85	6120.64	1.08218	
1289	ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [source:swissprot;acc:p51812]	Subtracted	6079.45	6555.4	475.95	
1290	calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [source:swissprot;acc:q13555]	Subtracted	6079.45	6555.4	475.95	
1290	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [source:swissprot;acc:q9hcs2]	Divided	5655.85	6120.64	1.08218	
1291	calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [source:swissprot;acc:q13557]	Subtracted	6079.46	6555.41	475.95	
1291	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:p78329]	Divided	5655.85	6120.64	1.08218	
1292	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [source:swissprot;acc:q9hbi6]	Divided	5655.85	6120.64	1.08218	
1292	signal-induced proliferation-associated 1-like 1. [source:refseq;acc:nm_015556]	Subtracted	6079.45	6555.4	475.95	
1293	dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [source:sptrembl;acc:q9ntl5]	Divided	5655.85	6120.64	1.08218	
1293	ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [source:swissprot;acc:q15418]	Subtracted	6079.46	6555.41	475.95	
1294	atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [source:swissprot;acc:p28288]	Subtracted	6079.46	6555.41	475.95	
1294	sestrin 3. [source:swissprot;acc:p58005]	Divided	5655.85	6120.65	1.08218	
1295	cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [source:swissprot;acc:p13584]	Divided	5655.85	6120.64	1.08218	
1295	glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [source:swissprot;acc:q92947]	Subtracted	6079.46	6555.41	475.95	
1296	flotillin-1. [source:swissprot;acc:o75955]	Divided	5655.85	6120.64	1.08218	
1296	histidine ammonia-lyase (ec 4.3.1.3) (histidase). [source:swissprot;acc:p42357]	Subtracted	6079.46	6555.41	475.95	
1297	ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [source:swissprot;acc:q9uk32]	Subtracted	6079.45	6555.4	475.95	
1297	sestrin 2 (hi95). [source:swissprot;acc:p58004]	Divided	5655.85	6120.65	1.08218	
1298	ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [source:swissprot;acc:q15349]	Subtracted	6079.45	6555.4	475.95	
1298	sestrin 1 (p53-regulated protein pa26). [source:swissprot;acc:q9y6p5]	Divided	5655.85	6120.62	1.08218	
1299	calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [source:swissprot;acc:q9uqm7]	Subtracted	6079.45	6555.4	475.95	
1299	cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [source:swissprot;acc:q15070]	Divided	5589.33	6047.9	1.08204	
1300	60s ribosomal protein l34, mitochondrial precursor (l34mt). [source:swissprot;acc:q9bq48]	Divided	5589.33	6047.9	1.08204	
1300	calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [source:swissprot;acc:q13554]	Subtracted	6079.46	6555.41	475.95	
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	

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/