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 2451 to 2500 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
307	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	Measured	0	4159.87	3775.43	1.10183
	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791]	Squared	1	28896.4	36766.8	1.27237
	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	Rooted	0	53.5229	49.96	1.07132
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	Ranked	1	242.153	266.673	1.10126
	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	Measured		12365.2	14824.9	1.19892
	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	Rooted		50.4687	45.2733	1.11476
308	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7]	Squared		30596.2	38919.9	1.27205
	60s ribosomal protein l34. [swissprot;acc:p49207]	Ranked		242.153	266.673	1.10126
	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]	Rooted		50.4687	45.2733	1.11476
	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	Rooted	0	22.112	20.6871	1.06888
	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	Squared		4748.4	5654.56	1.19083
	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	Ranked		11414.1	12191.8	1.06814
	neurocalcin delta. [swissprot;acc:p29554]	Measured		702.055	773.218	1.10136
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Measured	1	4977.09	5966.44	1.19878
309	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	Squared	1	28900.8	36762.6	1.27203
	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	Squared	0	32413.7	38271.3	1.18071
	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	Ranked	0	13651	14572	1.06747
	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]	Ranked	1	242.153	266.673	1.10126
	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	Measured	1	4977.8	5966.14	1.19855
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	Rooted	0	30.0555	28.1651	1.06712
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Measured	0	1890.86	2081.91	1.10104
	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	Rooted	1	56.185	62.6036	1.11424
310	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	Ranked	0	9328.78	8741.55	1.06718
	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	Squared	1	28901.4	36762.1	1.27198
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Rooted	1	95.0526	85.3206	1.11406
	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	Rooted	0	47.6356	44.6445	1.067
	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	Ranked	1	242.153	266.673	1.10126
	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]	Measured	0	4755.32	4320.09	1.10075
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Squared	0	36765.6	31220.1	1.17763
	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. [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). [swissprot;acc:q9nrz5]	Squared	1	30566.4	38866.5	1.27154
	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Ranked	0	10253.5	9622.45	1.06558
	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Squared	0	1326.34	1126.71	1.17718
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Rooted	1	95.0526	85.3206	1.11406
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	Ranked		242.627	267.151	1.10108
	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Measured		4981.52	5964.58	1.19734
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Rooted	0	31.7744	33.8609	1.06567
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Measured	0	3117.17	2833.94	1.09994
312	60s ribosomal protein l3-like. [swissprot;acc:q92901]	Ranked	1	242.195	266.663	1.10103
	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	Rooted	0	25.2821	26.9306	1.0652
	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	Measured		3455.43	3800.29	1.0998
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Ranked		11959.8	12731.1	1.06449
	methyltransferase like 2. [refseq;acc:nm_018396]	Squared	1	71576.8	56326.7	1.27074
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Rooted		95.0526	85.3206	1.11406
	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Measured		4598.21	5500.48	1.19622
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]	Squared	0	25325.5	29804.9	1.17687
313	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	Measured	0	6131.07	6739.34	1.09921
	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]	Squared	1	71576.8	56326.7	1.27074
	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). [swissprot;acc:p14061]	Rooted	0	25.2821	26.9306	1.0652
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Ranked	0	11935.6	12698.9	1.06395

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/