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 51 to 100 of 7460 in total

Value Type	Measured
Interaction Map	High confidence

Rank	description	Network Comparison Type	Filtered	red	green	network_comparison	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Divided	1	398.5	1281.5	3.21581	
13	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	Subtracted	1	21591.5	27904.5	6313	
14	apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	Subtracted	0	10817.1	12125.1	1308	
14	cyclin h (mo15-associated protein) (p37) (p34). [source:swissprot;acc:p51946]	Divided	0	130.512	6.50325	20.0687	
14	myosin vc (myosin 5c). [source:swissprot;acc:q9nqx4]	Subtracted	1	21591.5	27904.5	6313	
14	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Divided	1	398.5	1281.5	3.21581	
15	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Subtracted	1	21591.5	27904.5	6313	
15	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	Divided	0	10	156	15.6	
15	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	Subtracted	0	7981.68	6685.11	1296.57	
15	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Divided	1	2671	871	3.06659	
16	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Subtracted	1	24260.3	18172.1	6088.2	
16	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	Subtracted	0	8852.4	7572.88	1279.52	
16	protein transport protein sec24c (sec24-related protein c). [source:swissprot;acc:p53992]	Divided	0	1	15	15	
16	protein x 0004. [source:refseq;acc:nm_016301]	Divided	1	2671	871	3.06659	
17	ba271b5.1 (similar to ribosomal protein s7). [source:sptrembl;acc:q9h1s9]	Subtracted	0	11223	12473	1250	
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	Divided	1	460	1365	2.96739	
17	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Subtracted	1	24255.7	18168.9	6086.8	
17	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	Divided	0	859	58	14.8103	
18	60s ribosomal protein l37a. [source:swissprot;acc:p12751]	Divided	0	305.45	26.1599	11.6763	
18	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [source:swissprot;acc:q9nyg5]	Subtracted	0	15411.3	14167	1244.3	
18	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Subtracted	1	24255.7	18168.9	6086.8	
18	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	Divided	1	677.5	1865.5	2.75351	
19	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	Divided	0	305.45	26.1599	11.6763	
19	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Subtracted	1	24250	18164.9	6085.1	
19	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [source:sptrembl;acc:q9uge0]	Subtracted	0	1593	2804	1211	
19	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	Divided	1	677.5	1865.5	2.75351	
20	ero1-like. [source:refseq;acc:nm_014584]	Divided	0	82	0.00001	8200000	
20	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Subtracted	1	23421.5	17580.4	5841.1	
20	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [source:swissprot;acc:q9h361]	Subtracted	0	8763	7608	1155	
20	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	Divided	1	677.5	1865.5	2.75351	
21	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [source:swissprot;acc:q15485]	Divided	1	677.5	1865.5	2.75351	
21	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	Subtracted	1	23693.7	18263	5430.7	
21	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [source:swissprot;acc:q96gm5]	Subtracted	0	6804.88	5690.63	1114.25	
21	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	Divided	0	118.878	17.6611	6.73106	
22	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	Subtracted	1	23693.7	18263	5430.7	
22	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [source:refseq;acc:nm_030949]	Divided	1	677.5	1865.5	2.75351	
22	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	Divided	0	60	0.00001	6000000	
22	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [source:swissprot;acc:o00268]	Subtracted	0	31122	30022.4	1099.6	
23	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:o00757]	Subtracted	0	6596.23	5540.2	1056.03	
23	gbp protein isoform a. [source:refseq;acc:nm_017870]	Divided	1	699.76	1894.39	2.7072	
23	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [source:swissprot;acc:q9byb4]	Divided	0	0.00001	59	5900000	
23	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Subtracted	1	23693.7	18263	5430.7	
24	fos-related antigen 2. [source:swissprot;acc:p15408]	Subtracted	0	3233.86	2208.1	1025.76	
24	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	Subtracted	1	23693.7	18263	5430.7	
24	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	Divided	1	950.561	2108.52	2.21818	
24	ptd016 protein. [source:refseq;acc:nm_016125]	Divided	0	30	158	5.26667	
25	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	Subtracted	0	459.5	1377	917.5	
25	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	Divided	1	1833.01	892.67	2.0534	
25	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	Subtracted	1	23693.7	18263	5430.7	
25	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [source:swissprot;acc:o75110]	Divided	0	148	773	5.22297	

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/