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

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Showing element 151 to 200 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
10	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Squared	Subtracted	1	219048	129762	89286
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Measured		0	7830.62	6193.07	1637.55
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Measured		1	21185	28492	7307
	protein x 0004. [refseq;acc:nm_016301]	Ranked	Divided	1	212	309	1.45755
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		Subtracted	0	20989	12479	8510
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]		Subtracted	1	288	362	74
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Measured	Divided		398.5	1281.5	3.21581
		Squared			37.5863	388.696	10.3414
		Rooted			19.9625	35.798	1.79326
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Rooted	Subtracted		51.6817	29.5127	22.169
11	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Ranked		0	12170.7	20670.6	8499.9
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Measured		0	5734.28	7252.02	1517.74
	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Measured	Divided	1	398.5	1281.5	3.21581
		Squared			37.5863	388.696	10.3414
		Rooted			19.9625	35.798	1.79326
	db83 protein. [swissprot;acc:p57088]	Ranked	Subtracted		288	362	74
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Rooted		0	12.3693	25.7294	13.3601
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Squared		1	219048	129762	89286
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Measured		1	21185	28492	7307
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Squared		0	54383.4	34012.2	20371.2
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Ranked	Divided	0	11627	6248	1.86092
	protein x 0004. [refseq;acc:nm_016301]	Rooted	Subtracted	1	51.6817	29.5127	22.169
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked	Divided	1	337	232	1.45259
	sedlin. [swissprot;acc:o14582]	Squared		0	0.00001	0.437633	43763.3
	sedlin. [swissprot;acc:o14582]	Rooted			0.00001	6.55744	655744
	serpin b12. [swissprot;acc:q96p63]	Measured			199.549	5.56738	35.8425
12	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	Rooted	Subtracted		21.3967	34.6716	13.2749
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Squared			1.73869	19295.9	19294.2
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Rooted		1	80.4705	101.526	21.0555
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Measured		0	5629.62	7099.51	1469.89
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Measured	Divided	1	398.5	1281.5	3.21581
		Squared			37.5863	388.696	10.3414
		Rooted			19.9625	35.798	1.79326
	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	Ranked		0	9429.18	5208.84	1.81023
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Ranked	Subtracted	1	266.856	336.233	69.377
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Measured	Divided	0	199.249	5.71669	34.8539
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Squared	Subtracted	1	219048	129762	89286
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured	Subtracted		34190.9	40795.8	6604.9
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Ranked	Divided		337	232	1.45259
	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]	Ranked	Subtracted	0	19403	11267	8136
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Squared	Divided		0.00001	0.437633	43763.3
		Rooted			0.00001	6.55744	655744
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Measured			1363	47	29
		Measured	Subtracted		1363	47	1316
	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Rooted		1	80.4705	101.526	21.0555
	cab2. [refseq;acc:nm_033419]	Rooted		0	0	13.1909	13.1909
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Measured	Divided	1	398.5	1281.5	3.21581
		Squared			37.5863	388.696	10.3414
		Rooted			19.9625	35.798	1.79326
	dok-like protein. [refseq;acc:nm_024872]	Squared		0	0.289941	0.00001	28994.1

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/