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 2508 to 2557 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
314	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	Ranked	1	244.126	268.604	1.10027
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Rooted	1	95.0526	85.3206	1.11406
	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	Squared	0	6027.87	7086.08	1.17555
	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	Measured	1	21632.5	18090	1.19583
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]		0	5302.7	4827.7	1.09839
315	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]			1212.82	1104.61	1.09796
	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	Rooted		17.9172	16.833	1.06441
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	Squared		36059.4	30745.3	1.17284
	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	Ranked	1	244.126	268.604	1.10027
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Rooted		95.0526	85.3206	1.11406
	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	Squared		71576.8	56326.7	1.27074
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Ranked	0	12121.6	12887.6	1.06319
	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	Measured	1	21370.8	17896.5	1.19413
316	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	Squared	0	8620.27	7355.46	1.17196
	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	Measured		525	576	1.09714
	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	Ranked		10768.5	11444	1.06273
	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	Rooted	1	95.0526	85.3206	1.11406
	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	Squared		28918.3	36746	1.27068
	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	Ranked		242.694	267.017	1.10022
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Measured		21370.8	17896.5	1.19413
	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	Rooted	0	41.4068	38.9073	1.06424
317	adiponectin receptor 2. [refseq;acc:nm_024551]	Measured	1	3153.1	3762.56	1.19329
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Rooted	1	95.0526	85.3206	1.11406
	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409]	Rooted	0	7.79521	7.32908	1.0636
	lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]	Squared		237.082	277.442	1.17024
	my016 protein. [sptrembl;acc:q9h3k6]	Measured		1770.21	1615.47	1.09579
	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232]	Squared	1	33982.3	43159.1	1.27005
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Ranked	0	19939	18778	1.06183
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Ranked	1	224.445	204.044	1.09998
318	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189]	Rooted	0	7.80086	7.3344	1.0636
	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	Ranked	1	242.011	266.18	1.09987
	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388]	Squared		46739.9	59134.5	1.26518
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Rooted		95.0526	85.3206	1.11406
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured		34190.9	40795.8	1.19318
	protein cgi-147. [swissprot;acc:q9y3e5]	Measured	0	8396.12	9192.38	1.09484
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Squared		7372.32	6325.27	1.16553
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]	Ranked		8918.54	9465.32	1.06131
319	60s ribosomal protein l19. [swissprot;acc:p14118]	Ranked	1	240.73	264.729	1.09969
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Measured	0	1388.45	1268.19	1.09483
	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410]	Rooted	0	7.78379	7.31834	1.0636
	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]	Squared	1	46739.9	59134.5	1.26518
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Measured		20911	24908.5	1.19117
	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	Rooted		49.0663	54.4978	1.1107
	scratch; scratch 1. [refseq;acc:nm_031309]	Squared	0	5976.46	5135.5	1.16375
	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]	Ranked	0	8918.54	9465.32	1.06131
320	40s ribosomal protein s29. [swissprot;acc:p30054]	Rooted	1	50.2784	45.294	1.11005
	adp-ribosylation factor 3. [swissprot;acc:p16587]	Ranked	0	11627.8	10958.2	1.0611
	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	Squared	0	5127.13	5964.46	1.16331
	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	Ranked	1	241.892	265.96	1.0995
	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099]	Squared	1	87971.9	69563.1	1.26463

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/