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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

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Showing element 101 to 150 of 19268 in total

Value Type

: Measured

Rank	green	description	network_comparison	Network Comparison Type	Interaction Map	red	Filtered
13	2959.19	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	1.5351	Divided	Low confidence	1927.68	1
	3953.32	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	992.25	Subtracted		2961.07	0
	17572.7	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	2108.6			15464.1	1
	27904.5	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	6313		High confidence	21591.5	1
14	6.50325	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	20.0687	Divided	High confidence	130.512	0
	59	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]	5900000		Low confidence	0.00001	0
	1281.5	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	3.21581		High confidence	398.5	1
	2998.1	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	1.51983		Low confidence	1972.65	1
	12125.1	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	1308	Subtracted	High confidence	10817.1	0
	16295.1	rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]	940.4		Low confidence	17235.5	0
	17572.7	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	2108.6		Low confidence	15464.1	1
	27904.5	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	6313		High confidence	21591.5	1
15	156	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]	15.6	Divided		10	0
	871	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	3.06659			2671	1
	2740.13	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	5.64642		Low confidence	485.286	0
	3007.85	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	1.51612			1983.91	1
	4823.8	myotubularin related protein 8. [refseq;acc:nm_017677]	935.2	Subtracted		3888.6	0
	6685.11	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	1296.57		High confidence	7981.68	0
	17572.7	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	2108.6		Low confidence	15464.1	1
	27904.5	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	6313		High confidence	21591.5	1
16	15	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	15	Divided	High confidence	1	0
	704.5	protein kinase, lysine deficient 3. [refseq;acc:nm_020922]	5.636		Low confidence	125	0
	871	protein x 0004. [refseq;acc:nm_016301]	3.06659		High confidence	2671	1
	7572.88	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	1279.52	Subtracted	High confidence	8852.4	0
	9808	vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21]	881.67		Low confidence	8926.33	0
	17572.7	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	2108.6		Low confidence	15464.1	1
	18172.1	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	6088.2		High confidence	24260.3
	28492	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	1.34491	Divided	Low confidence	21185
17	58	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14.8103		High confidence	859	0
	158	ptd016 protein. [refseq;acc:nm_016125]	5.26667		Low confidence	30	0
	1365	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	2.96739		High confidence	460	1
	5837.83	ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08]	878.41	Subtracted	Low confidence	4959.42	0
	12473	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	1250		High confidence	11223	0
	17572.7	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	2108.6		Low confidence	15464.1	1
	18168.9	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	6086.8		High confidence	24255.7
	28492	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	1.34491	Divided	Low confidence	21185
18	19	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	5.21053		Low confidence	99	0
	26.1599	60s ribosomal protein l37a. [swissprot;acc:p12751]	11.6763		High confidence	305.45
	58	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	801	Subtracted	Low confidence	859
	1865.5	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	2.75351	Divided	High confidence	677.5	1
	7251	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	1.32027	Divided	Low confidence	5492.04	1
	14167	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	1244.3	Subtracted	High confidence	15411.3	0
	17572.7	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	2108.6		Low confidence	15464.1	1
	18168.9	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	6086.8		High confidence	24255.7	1
19	26.1599	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]	11.6763	Divided	High confidence	305.45	0
	662	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	4.3268		Low confidence	153	0
	1865.5	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	2.75351		High confidence	677.5	1
	2407.27	fos-related antigen 2. [swissprot;acc:p15408]	798.71	Subtracted	Low confidence	3205.98	0
	2804	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	1211	Subtracted	High confidence	1593	0
	3915.4	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]	1.29112	Divided	Low confidence	3032.56	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/