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 2518 to 2567 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1259	serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [source:swissprot;acc:p51956]	Subtracted	5961.97	6443.07	481.1	
1260	glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [source:swissprot;acc:p04406]	Subtracted	5961.97	6443.07	481.1	
1260	rad54-like protein; rad54 homolog. [source:refseq;acc:nm_003579]	Divided	5754.84	6232.83	1.08306	
1261	43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [source:swissprot;acc:q13702]	Subtracted	6160.06	6640.78	480.72	
1261	epidermal growth factor receptor kinase substrate eps8. [source:swissprot;acc:q12929]	Divided	5685.34	6157.53	1.08305	
1262	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [source:swissprot;acc:q15765]	Subtracted	5207.39	5687.2	479.81	
1262	serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [source:swissprot;acc:q9upe1]	Divided	5894.47	6383.73	1.083	
1263	gtp binding protein 2. [source:refseq;acc:nm_019096]	Divided	5894.47	6383.73	1.083	
1263	prefoldin subunit 2 (hspc231). [source:swissprot;acc:q9uhv9]	Subtracted	5207.39	5687.2	479.81	
1264	cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [source:swissprot;acc:q99941]	Divided	5894.47	6383.73	1.083	
1264	uxt protein (ubiquitously expressed transcript protein) (hspc024). [source:swissprot;acc:q9ubk9]	Subtracted	5207.39	5687.2	479.81	
1265	6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [source:swissprot;acc:p08237]	Subtracted	4250.54	4729.67	479.13	
1265	dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [source:refseq;acc:nm_012135]	Divided	5894.47	6383.73	1.083	
1266	mitotic checkpoint protein bub3. [source:swissprot;acc:o43684]	Subtracted	5470.44	5949.49	479.05	
1266	sfrs protein kinase 2 isoform b. [source:refseq;acc:nm_182691]	Divided	5894.47	6383.73	1.083	
1267	cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [source:swissprot;acc:p18850]	Divided	5894.47	6383.73	1.083	
1267	zinc finger protein 207. [source:swissprot;acc:o43670]	Subtracted	5470.44	5949.49	479.05	
1268	6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [source:swissprot;acc:p17858]	Subtracted	4250.18	4729.12	478.94	
1268	sfrs protein kinase 1; sr protein kinase 1. [source:refseq;acc:nm_003137]	Divided	5894.47	6383.73	1.083	
1269	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [source:swissprot;acc:o75521]	Subtracted	7048.79	7527.42	478.63	
1269	xap-5 protein (hxc-26 protein). [source:swissprot;acc:q14320]	Divided	5894.47	6383.73	1.083	
1270	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	Subtracted	5654.53	6132.76	478.23	
1270	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]	Divided	5685.08	6156.48	1.08292	
1271	mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [source:swissprot;acc:o60566]	Divided	5528.65	5985.58	1.08265	
1271	retinoic acid induced 17; pias-like protein hzimp10. [source:refseq;acc:nm_020338]	Subtracted	5654.54	6132.69	478.15	
1272	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Divided	5528.65	5985.58	1.08265	
1272	rad54-like protein; rad54 homolog. [source:refseq;acc:nm_003579]	Subtracted	5754.84	6232.83	477.99	
1273	phafin 2; ph and fyve domain-containing protein 2. [source:refseq;acc:nm_024613]	Divided	5885	6371.14	1.08261	
1273	proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [source:swissprot;acc:o14818]	Subtracted	6216.12	6693.38	477.26	
1274	3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [source:swissprot;acc:p18405]	Divided	5885	6371.14	1.08261	
1274	megf6 (fragment). [source:sptrembl;acc:o75095]	Subtracted	5980.41	6457.51	477.1	
1275	3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [source:swissprot;acc:p31213]	Divided	5885	6371.14	1.08261	
1275	proteasome subunit alpha type 7-like (ec 3.4.25.1). [source:swissprot;acc:q8taa3]	Subtracted	6216.13	6693.13	477	
1276	6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [source:swissprot;acc:p52209]	Subtracted	5988.06	6464.94	476.88	
1276	peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [source:swissprot;acc:q9nr77]	Divided	6437.99	6969.67	1.08258	
1277	heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [source:swissprot;acc:p54652]	Divided	6437.99	6969.67	1.08258	
1277	serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [source:swissprot;acc:p34896]	Subtracted	5418.33	5895.2	476.87	
1278	eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [source:swissprot;acc:o75821]	Subtracted	4131.04	4607.9	476.86	
1278	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [source:swissprot;acc:p08107]	Divided	6437.99	6969.67	1.08258	
1279	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [source:swissprot;acc:q14152]	Subtracted	4131.04	4607.9	476.86	
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	

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/