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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 2358 to 2407 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1179	solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [source:refseq;acc:nm_006749]	Divided	4392.63	4776.19	1.08732	
1180	farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [source:swissprot;acc:p14324]	Divided	4392.63	4776.19	1.08732	
1180	tata element modulatory factor (tmf). [source:swissprot;acc:p82094]	Subtracted	5412.23	5913.4	501.17	
1181	protocadherin 15 precursor. [source:swissprot;acc:q96qu1]	Divided	4392.63	4776.19	1.08732	
1181	scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [source:refseq;acc:nm_020680]	Subtracted	5412.23	5913.4	501.17	
1182	nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [source:swissprot;acc:p52948]	Subtracted	5412.23	5913.4	501.17	
1182	solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [source:refseq;acc:nm_005415]	Divided	4392.63	4776.19	1.08732	
1183	ammecr1 protein. [source:refseq;acc:nm_015365]	Subtracted	5412.23	5913.4	501.17	
1183	lipocalin-interacting membrane receptor. [source:refseq;acc:nm_018113]	Divided	4392.63	4776.19	1.08732	
1184	mrna-associated protein mrnp 41 (rae1 protein homolog). [source:swissprot;acc:p78406]	Subtracted	5412.23	5913.4	501.17	
1184	zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [source:swissprot;acc:p08151]	Divided	4392.63	4776.19	1.08732	
1185	peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [source:swissprot;acc:o75381]	Subtracted	6522.96	7023.77	500.81	
1185	suppressor of fused. [source:refseq;acc:nm_016169]	Divided	4392.63	4776.19	1.08732	
1186	mitochondrial gtp binding protein isoform v. [source:refseq;acc:nm_032620]	Subtracted	6222.8	6723.54	500.74	
1186	zinc finger protein gli3. [source:swissprot;acc:p10071]	Divided	4392.63	4776.19	1.08732	
1187	leucyl-trna synthetase. [source:refseq;acc:nm_020117]	Subtracted	5417.06	5917.79	500.73	
1187	limb region 1 protein; limb region 1. [source:refseq;acc:nm_022458]	Divided	4392.63	4776.19	1.08732	
1188	gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [source:swissprot;acc:p20142]	Divided	4392.63	4776.19	1.08732	
1188	probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [source:swissprot;acc:q15031]	Subtracted	5417.07	5917.79	500.72	
1189	nuclear factor, interleukin 3 regulated. [source:refseq;acc:nm_005384]	Subtracted	5869.24	6367.8	498.56	
1189	zinc finger protein gli2 (tax helper protein). [source:swissprot;acc:p10070]	Divided	4392.63	4776.19	1.08732	
1190	mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [source:swissprot;acc:q13257]	Divided	6599.84	7174.29	1.08704	
1190	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [source:swissprot;acc:q99471]	Subtracted	4982.81	5480.91	498.1	
1191	prefoldin subunit 6 (protein ke2). [source:swissprot;acc:o15212]	Subtracted	4982.81	5480.91	498.1	
1191	probable cation-transporting atpase 1 (ec 3.6.1.-). [source:swissprot;acc:q9nq11]	Divided	6599.84	7174.29	1.08704	
1192	immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [source:swissprot;acc:q14197]	Subtracted	5364.32	5862.09	497.77	
1192	tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [source:swissprot;acc:p20226]	Divided	6599.84	7174.29	1.08704	
1193	putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [source:swissprot;acc:o75153]	Divided	5464.9	5940.16	1.08697	
1193	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [source:refseq;acc:nm_003900]	Subtracted	6322.75	6820.5	497.75	
1194	nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [source:swissprot;acc:p22307]	Subtracted	6322.75	6820.5	497.75	
1194	t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [source:swissprot;acc:p48643]	Divided	8425.35	7751.57	1.08692	
1195	protein ad-016 (protein cgi-116) (x0009). [source:swissprot;acc:q9y3c0]	Subtracted	6110.09	6607.81	497.72	
1195	similar to trna synthetase class ii. [source:refseq;acc:nm_152268]	Divided	5439.56	5911.24	1.08671	
1196	kappa b-ras 1. [source:refseq;acc:nm_020345]	Divided	5721.19	6217.2	1.0867	
1196	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [source:refseq;acc:nm_015975]	Subtracted	7659.42	8156.79	497.37	
1197	i-kappa-b-interacting ras-like protein 2. [source:refseq;acc:nm_017595]	Divided	5721.19	6217.2	1.0867	
1197	tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [source:swissprot;acc:q9y3q8]	Subtracted	5873.56	6370.31	496.75	
1198	snare associated protein snapin. [source:refseq;acc:nm_012437]	Divided	5721.19	6217.2	1.0867	
1198	sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [source:refseq;acc:nm_003676]	Subtracted	5873.56	6370.31	496.75	
1199	peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [source:swissprot;acc:q9uj68]	Subtracted	5489.99	5986.63	496.64	
1199	serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [source:swissprot;acc:p34897]	Divided	5449.48	5921.77	1.08667	
1200	phosphoserine aminotransferase (ec 2.6.1.52) (psat). [source:swissprot;acc:q9y617]	Subtracted	5489.99	5986.63	496.64	
1200	xylulokinase homolog; xylulokinase (h. influenzae) homolog. [source:refseq;acc:nm_005108]	Divided	5950.27	6465.72	1.08663	
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	

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/