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 network_comparison red

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

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/