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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2458 to 2507 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
308	60s ribosomal protein l34. [source:swissprot;acc:p49207]	Ranked	1	242.153	266.673	1.10126	
308	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	Rooted	1	50.4687	45.2733	1.11476	
308	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [source:swissprot;acc:p15104]	Rooted	0	22.112	20.6871	1.06888	
308	histone deacetylase 2 (hd2). [source:swissprot;acc:q92769]	Squared	0	4748.4	5654.56	1.19083	
308	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [source:swissprot;acc:q15811]	Ranked	0	11414.1	12191.8	1.06814	
308	neurocalcin delta. [source:swissprot;acc:p29554]	Measured	0	702.055	773.218	1.10136	
308	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	Measured	1	4977.09	5966.44	1.19878	
309	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Squared	1	28900.8	36762.6	1.27203	
309	dyskerin (nucleolar protein nap57) (cbf5 homolog). [source:swissprot;acc:o60832]	Squared	0	32413.7	38271.3	1.18071	
309	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	Ranked	0	13651	14572	1.06747	
309	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	Ranked	1	242.153	266.673	1.10126	
309	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	Measured	1	4977.8	5966.14	1.19855	
309	small glutamine rich protein with tetratricopeptide repeats 2. [source:refseq;acc:nm_019072]	Rooted	0	30.0555	28.1651	1.06712	
309	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	Measured	0	1890.86	2081.91	1.10104	
309	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [source:swissprot;acc:q9y333]	Rooted	1	56.185	62.6036	1.11424	
310	glycine cleavage system h protein, mitochondrial precursor. [source:swissprot;acc:p23434]	Ranked	0	9328.78	8741.55	1.06718	
310	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Squared	1	28901.4	36762.1	1.27198	
310	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Rooted	1	95.0526	85.3206	1.11406	
310	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [source:swissprot;acc:q9y466]	Rooted	0	47.6356	44.6445	1.067	
310	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	Ranked	1	242.153	266.673	1.10126	
310	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [source:swissprot;acc:p00491]	Measured	0	4755.32	4320.09	1.10075	
310	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	Squared	0	36765.6	31220.1	1.17763	
310	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [source:refseq;acc:nm_005146]	Measured	1	4909.79	5878.79	1.19736	
311	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [source:swissprot;acc:q9nrz5]	Squared	1	30566.4	38866.5	1.27154	
311	60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	Ranked	0	10253.5	9622.45	1.06558	
311	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [source:swissprot;acc:o76031]	Squared	0	1326.34	1126.71	1.17718	
311	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Rooted	1	95.0526	85.3206	1.11406	
311	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	Ranked	1	242.627	267.151	1.10108	
311	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	Measured	1	4981.52	5964.58	1.19734	
311	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	Rooted	0	31.7744	33.8609	1.06567	
311	transcription factor cp2; transcription factor cp2, alpha globin. [source:refseq;acc:nm_005653]	Measured	0	3117.17	2833.94	1.09994	
312	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	Ranked	1	242.195	266.663	1.10103	
312	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [source:swissprot;acc:p07741]	Rooted	0	25.2821	26.9306	1.0652	
312	dyskerin (nucleolar protein nap57) (cbf5 homolog). [source:swissprot;acc:o60832]	Measured	0	3455.43	3800.29	1.0998	
312	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	Ranked	0	11959.8	12731.1	1.06449	
312	methyltransferase like 2. [source:refseq;acc:nm_018396]	Squared	1	71576.8	56326.7	1.27074	
312	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Rooted	1	95.0526	85.3206	1.11406	
312	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Measured	1	4598.21	5500.48	1.19622	
312	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [source:swissprot;acc:q9nyl9]	Squared	0	25325.5	29804.9	1.17687	
313	60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	Measured	0	6131.07	6739.34	1.09921	
313	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	Squared	1	71576.8	56326.7	1.27074	
313	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [source:swissprot;acc:p14061]	Rooted	0	25.2821	26.9306	1.0652	
313	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [source:swissprot;acc:p50150]	Ranked	0	11935.6	12698.9	1.06395	
313	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Rooted	1	95.0526	85.3206	1.11406	
313	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Measured	1	21644.2	18098.7	1.1959	
313	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Ranked	1	232.473	211.207	1.10069	
313	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [source:swissprot;acc:q9y5x1]	Squared	0	25325.5	29804.9	1.17687	
314	clathrin heavy chain 2 (clh-22). [source:swissprot;acc:p53675]	Ranked	0	10301.4	10957.5	1.06369	
314	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	Squared	1	71576.8	56326.7	1.27074	
314	kappa b-ras 1. [source:refseq;acc:nm_020345]	Rooted	0	21.0189	22.3788	1.0647	

Legend:
- Rank is the rank after comparing the two networks
- 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/