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 2401 to 2450 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1201	proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [source:swissprot;acc:p28074]	Subtracted	6523.17	7019.44	496.27	
1201	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [source:swissprot;acc:p23919]	Divided	6042.31	6565.03	1.08651	
1202	kappa b-ras 1. [source:refseq;acc:nm_020345]	Subtracted	5721.19	6217.2	496.01	
1202	porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [source:swissprot;acc:p08397]	Divided	4913.07	5337.95	1.08648	
1203	geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [source:swissprot;acc:o95749]	Divided	4322.65	4696.04	1.08638	
1203	i-kappa-b-interacting ras-like protein 2. [source:refseq;acc:nm_017595]	Subtracted	5721.19	6217.2	496.01	
1204	snare associated protein snapin. [source:refseq;acc:nm_012437]	Subtracted	5721.19	6217.2	496.01	
1204	suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [source:swissprot;acc:o15524]	Divided	5946.33	6459.79	1.08635	
1205	glia maturation factor gamma (gmf-gamma). [source:swissprot;acc:o60234]	Divided	5946.33	6459.79	1.08635	
1205	phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [source:swissprot;acc:q9nsd9]	Subtracted	5462.88	5958.12	495.24	
1206	asc-1 complex subunit p100. [source:refseq;acc:nm_032204]	Divided	5946.33	6459.79	1.08635	
1206	synaptotagmin xii (sytxii). [source:swissprot;acc:q8iv01]	Subtracted	5460.49	5954.62	494.13	
1207	fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [source:swissprot;acc:p20071]	Divided	5946.33	6459.79	1.08635	
1207	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [source:swissprot;acc:q9y466]	Subtracted	6105.93	6599.41	493.48	
1208	meiotic recombination protein dmc1/lim15 homolog. [source:swissprot;acc:q14565]	Divided	5913.73	6423.98	1.08628	
1208	orphan nuclear receptor tr2. [source:swissprot;acc:p13056]	Subtracted	6105.69	6599.06	493.37	
1209	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]	Divided	5420.87	5887.53	1.08609	
1209	dead-box protein 4 (vasa homolog). [source:swissprot;acc:q9nqi0]	Subtracted	5147.9	5641.25	493.35	
1210	mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [source:swissprot;acc:q15750]	Subtracted	6051.23	6544.17	492.94	
1210	trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [source:swissprot;acc:q9nvh6]	Divided	6410.73	6962.22	1.08603	
1211	gtp-binding protein era homolog (hera) (fragment). [source:swissprot;acc:o75616]	Divided	6410.73	6962.22	1.08603	
1211	similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [source:refseq;acc:nm_145245]	Subtracted	5807.83	6300.47	492.64	
1212	ecotropic viral integration site 5; neuroblastoma stage 4s gene. [source:refseq;acc:nm_005665]	Subtracted	5807.83	6300.47	492.64	
1212	hiv-1 rev binding protein 2; rev interacting protein. [source:refseq;acc:nm_007043]	Divided	4077.89	4428.28	1.08592	
1213	branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [source:swissprot;acc:p54687]	Divided	5890.62	6396.53	1.08588	
1213	g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [source:swissprot;acc:p15170]	Subtracted	6140.18	6632.24	492.06	
1214	mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [source:swissprot;acc:o43318]	Divided	6001.16	6515.9	1.08577	
1214	nucleolar protein nop56 (nucleolar protein 5a). [source:swissprot;acc:o00567]	Subtracted	3879.99	4371.24	491.25	
1215	branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [source:swissprot;acc:o15382]	Divided	5892.05	6397.28	1.08575	
1215	cyclin m2; ancient conserved domain protein 2. [source:refseq;acc:nm_017649]	Subtracted	5736.34	6226.88	490.54	
1216	cyclin m4; ancient conserved domain protein 4. [source:refseq;acc:nm_020184]	Subtracted	5736	6226.52	490.52	
1216	fibulin-2 precursor. [source:swissprot;acc:p98095]	Divided	8670.59	9412.9	1.08561	
1217	cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [source:swissprot;acc:p27708]	Divided	6021.21	6536.45	1.08557	
1217	tcd37 homolog; prune. [source:refseq;acc:nm_021222]	Subtracted	5735.95	6226.46	490.51	
1218	cyclin m1; ancient conserved domain protein 1. [source:refseq;acc:nm_020348]	Subtracted	5735.74	6226.23	490.49	
1218	cyclin m4; ancient conserved domain protein 4. [source:refseq;acc:nm_020184]	Divided	5736	6226.52	1.08552	
1219	cyclin m3; ancient conserved domain protein 3. [source:refseq;acc:nm_017623]	Subtracted	5735.65	6226.13	490.48	
1219	tcd37 homolog; prune. [source:refseq;acc:nm_021222]	Divided	5735.95	6226.46	1.08552	
1220	cyclin m3; ancient conserved domain protein 3. [source:refseq;acc:nm_017623]	Divided	5735.65	6226.13	1.08551	
1220	mesoderm induction early response 1. [source:refseq;acc:nm_020948]	Subtracted	6291.89	6781.6	489.71	
1221	cyclin m2; ancient conserved domain protein 2. [source:refseq;acc:nm_017649]	Divided	5736.34	6226.88	1.08551	
1221	proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [source:swissprot;acc:p25788]	Subtracted	6291.89	6781.6	489.71	
1222	cyclin c. [source:swissprot;acc:p24863]	Subtracted	6200.93	6690.57	489.64	
1222	cyclin m1; ancient conserved domain protein 1. [source:refseq;acc:nm_020348]	Divided	5735.74	6226.23	1.08551	
1223	serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [source:swissprot;acc:q9upe1]	Subtracted	5894.47	6383.73	489.26	
1223	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [source:swissprot;acc:p51854]	Divided	6011.44	6524.55	1.08536	
1224	gtp binding protein 2. [source:refseq;acc:nm_019096]	Subtracted	5894.47	6383.73	489.26	
1224	splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [source:swissprot;acc:q15427]	Divided	4331.35	4700.91	1.08532	
1225	apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [source:refseq;acc:nm_014481]	Divided	5546.5	6019.57	1.08529	
1225	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]	Subtracted	5894.47	6383.73	489.26	

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/