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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Value Type Gene Interaction Map Rank description Filtered red green Network Comparison Type network_comparison

Results: HTML CSV LaTeX

Showing element 51 to 100 of 29840 in total

Value Type

: Measured
Interaction Map

: High confidence

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

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/