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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1280 to 1329 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
160	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Measured	1	23693.7	18263	1.29736	
161	adp-ribosylation factor 3. [source:swissprot;acc:p16587]	Rooted	0	14.8377	17.2252	1.16091	
161	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Ranked	0	5781.93	6660.63	1.15197	
161	glycine cleavage system h protein, mitochondrial precursor. [source:swissprot;acc:p23434]	Measured	0	903.767	1152.06	1.27473	
161	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Squared	1	173408	242989	1.40126	
161	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Measured	1	23693.7	18263	1.29736	
161	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Rooted	1	52.7642	61.9019	1.17318	
161	rap1 gtpase-activating protein 1 (rap1gap). [source:swissprot;acc:p47736]	Ranked	1	249.663	298.263	1.19466	
161	udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [source:swissprot;acc:p36537]	Squared	0	6123.28	3763.18	1.62716	
162	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Measured	0	5734.28	7252.02	1.26468	
162	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Rooted	1	52.7642	61.9019	1.17318	
162	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Squared	1	173408	242989	1.40126	
162	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	Rooted	0	9.27362	8	1.1592	
162	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Measured	1	23693.7	18263	1.29736	
162	nostrin. [source:refseq;acc:nm_052946]	Ranked	1	209.299	249.187	1.19058	
162	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	Ranked	0	12301.4	10680.5	1.15176	
162	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [source:swissprot;acc:p54855]	Squared	0	6123.28	3763.18	1.62716	
163	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	Ranked	1	209.299	249.187	1.19058	
163	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Rooted	1	52.7702	61.8915	1.17285	
163	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Squared	1	173408	242989	1.40126	
163	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Measured	1	23693.7	18263	1.29736	
163	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Measured	0	7830.62	6193.07	1.26442	
163	p28 ing5. [source:refseq;acc:nm_032329]	Squared	0	5071.93	3165.6	1.6022	
163	transcription factor cp2; transcription factor cp2, alpha globin. [source:refseq;acc:nm_005653]	Ranked	0	8409.21	9668.79	1.14979	
163	zinc finger protein 232. [source:swissprot;acc:q9uny5]	Rooted	0	17.1325	14.7869	1.15863	
164	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [source:swissprot;acc:p41181]	Measured	0	1711.55	1354.26	1.26383	
164	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	Squared	0	145.887	91.0551	1.60218	
164	dihydrofolate reductase (ec 1.5.1.3). [source:swissprot;acc:p00374]	Ranked	0	11971.7	10412.4	1.14975	
164	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	Squared	1	173408	242989	1.40126	
164	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	Ranked	1	209.299	249.187	1.19058	
164	mad protein (max dimerizer). [source:swissprot;acc:q05195]	Rooted	1	55.646	65.1534	1.17086	
164	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Measured	1	23693.7	18263	1.29736	
164	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [source:swissprot;acc:p17028]	Rooted	0	17.1341	14.7892	1.15855	
165	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	Ranked	1	209.299	249.187	1.19058	
165	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Squared	1	173408	242989	1.40126	
165	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Rooted	1	55.6486	65.1478	1.1707	
165	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Measured	1	23693.7	18263	1.29736	
165	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	Measured	0	1002.2	793.818	1.26251	
165	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Squared	0	54383.4	34012.2	1.59894	
165	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [source:swissprot;acc:p21108]	Ranked	0	13255.4	15183.2	1.14544	
165	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [source:swissprot;acc:q9ul58]	Rooted	0	17.1346	14.7899	1.15853	
166	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Measured	0	5629.62	7099.51	1.2611	
166	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	Ranked	1	209.299	249.187	1.19058	
166	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Squared	1	173408	242989	1.40126	
166	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [source:swissprot;acc:q16543]	Squared	0	220.039	350.57	1.59322	
166	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Rooted	1	55.6495	65.1458	1.17064	
166	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Measured	1	23693.7	18263	1.29736	
166	my016 protein. [source:sptrembl;acc:q9h3k6]	Ranked	0	5561.19	6366.91	1.14488	
166	zinc finger imprinted 2. [source:swissprot;acc:q9nzv7]	Rooted	0	17.1395	14.7969	1.15832	
167	dystrobrevin binding protein 1; dysbindin. [source:refseq;acc:nm_032122]	Squared	0	168.446	105.991	1.58925	

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/