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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 29840 in total

Value Type

: Measured
Interaction Map

: High confidence

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

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/