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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 101 to 150 of 77072 in total

Value Type

: Measured

Rank	Interaction Map	Network Comparison Type	description	Filtered	green	red	network_comparison
13	Low confidence	Divided	fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]	0	115.385	8.11997	14.21
		Divided	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	1	2959.19	1927.68	1.5351
		Subtracted	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	1	17572.7	15464.1	2108.6
		Subtracted	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	0	3953.32	2961.07	992.25
14	High confidence	Divided	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	0	6.50325	130.512	20.0687
		Divided	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	1	1281.5	398.5	3.21581
		Subtracted	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	0	12125.1	10817.1	1308
		Subtracted	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	1	27904.5	21591.5	6313
	Low confidence	Divided	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	59	0.00001	5900000
		Divided	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	1	2998.1	1972.65	1.51983
		Subtracted	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	1	17572.7	15464.1	2108.6
		Subtracted	rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]	0	16295.1	17235.5	940.4
15	High confidence	Divided	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	156	10	15.6
		Divided	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	1	871	2671	3.06659
		Subtracted	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	1	27904.5	21591.5	6313
		Subtracted	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	0	6685.11	7981.68	1296.57
	Low confidence	Divided	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	0	2740.13	485.286	5.64642
		Divided	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	1	3007.85	1983.91	1.51612
		Subtracted	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1	17572.7	15464.1	2108.6
		Subtracted	myotubularin related protein 8. [refseq;acc:nm_017677]	0	4823.8	3888.6	935.2
16	High confidence	Divided	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	0	15	1	15
		Divided	protein x 0004. [refseq;acc:nm_016301]	1	871	2671	3.06659
		Subtracted	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	1	18172.1	24260.3	6088.2
		Subtracted	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	0	7572.88	8852.4	1279.52
	Low confidence	Divided	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	1	28492	21185	1.34491
		Divided	protein kinase, lysine deficient 3. [refseq;acc:nm_020922]	0	704.5	125	5.636
		Subtracted	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	1	17572.7	15464.1	2108.6
		Subtracted	vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21]	0	9808	8926.33	881.67
17	High confidence	Divided	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	1	1365	460	2.96739
		Divided	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	58	859	14.8103
		Subtracted	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	0	12473	11223	1250
		Subtracted	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	1	18168.9	24255.7	6086.8
	Low confidence	Divided	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	1	28492	21185	1.34491
		Divided	ptd016 protein. [refseq;acc:nm_016125]	0	158	30	5.26667
		Subtracted	ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08]	0	5837.83	4959.42	878.41
		Subtracted	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	1	17572.7	15464.1	2108.6
18	High confidence	Divided	60s ribosomal protein l37a. [swissprot;acc:p12751]	0	26.1599	305.45	11.6763
		Divided	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1	1865.5	677.5	2.75351
		Subtracted	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	0	14167	15411.3	1244.3
		Subtracted	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	1	18168.9	24255.7	6086.8
	Low confidence	Divided	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	0	19	99	5.21053
		Divided	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	1	7251	5492.04	1.32027
		Subtracted	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	1	17572.7	15464.1	2108.6
		Subtracted	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	58	859	801
19	High confidence	Divided	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	26.1599	305.45	11.6763
		Divided	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	1	1865.5	677.5	2.75351
		Subtracted	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	1	18164.9	24250	6085.1
		Subtracted	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	0	2804	1593	1211
	Low confidence	Divided	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	3915.4	3032.56	1.29112
	Low confidence	Divided	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	0	662	153	4.3268

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/