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

Results: HTML CSV LaTeX

Showing element 1232 to 1281 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
308	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	Measured	4977.09	5966.44	1.19878	
309	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Squared	28900.8	36762.6	1.27203	
309	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	Ranked	242.153	266.673	1.10126	
309	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	Measured	4977.8	5966.14	1.19855	
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	56.185	62.6036	1.11424	
310	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Squared	28901.4	36762.1	1.27198	
310	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Rooted	95.0526	85.3206	1.11406	
310	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	Ranked	242.153	266.673	1.10126	
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	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	30566.4	38866.5	1.27154	
311	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Rooted	95.0526	85.3206	1.11406	
311	protein translation factor sui1 homolog gc20. [source:swissprot;acc:o60739]	Ranked	242.627	267.151	1.10108	
311	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	Measured	4981.52	5964.58	1.19734	
312	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	Ranked	242.195	266.663	1.10103	
312	methyltransferase like 2. [source:refseq;acc:nm_018396]	Squared	71576.8	56326.7	1.27074	
312	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Rooted	95.0526	85.3206	1.11406	
312	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Measured	4598.21	5500.48	1.19622	
313	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	Squared	71576.8	56326.7	1.27074	
313	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Rooted	95.0526	85.3206	1.11406	
313	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Measured	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	232.473	211.207	1.10069	
314	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	Squared	71576.8	56326.7	1.27074	
314	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [source:swissprot;acc:p53582]	Ranked	244.126	268.604	1.10027	
314	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Rooted	95.0526	85.3206	1.11406	
314	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	Measured	21632.5	18090	1.19583	
315	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [source:swissprot;acc:p50579]	Ranked	244.126	268.604	1.10027	
315	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	Rooted	95.0526	85.3206	1.11406	
315	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [source:swissprot;acc:q92824]	Squared	71576.8	56326.7	1.27074	
315	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	Measured	21370.8	17896.5	1.19413	
316	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Rooted	95.0526	85.3206	1.11406	
316	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Squared	28918.3	36746	1.27068	
316	protein translation factor sui1 homolog (sui1iso1). [source:swissprot;acc:p41567]	Ranked	242.694	267.017	1.10022	
316	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	Measured	21370.8	17896.5	1.19413	
317	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Measured	3153.1	3762.56	1.19329	
317	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	Rooted	95.0526	85.3206	1.11406	
317	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [source:swissprot;acc:q13232]	Squared	33982.3	43159.1	1.27005	
317	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	Ranked	224.445	204.044	1.09998	
318	mitochondrial 60s ribosomal protein l3 (l3mt). [source:swissprot;acc:p09001]	Ranked	242.011	266.18	1.09987	
318	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [source:swissprot;acc:q15388]	Squared	46739.9	59134.5	1.26518	
318	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Rooted	95.0526	85.3206	1.11406	
318	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Measured	34190.9	40795.8	1.19318	
319	60s ribosomal protein l19. [source:swissprot;acc:p14118]	Ranked	240.73	264.729	1.09969	
319	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [source:swissprot;acc:p40855]	Squared	46739.9	59134.5	1.26518	
319	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	Measured	20911	24908.5	1.19117	
319	saccharomyces cerevisiae nip7p homolog. [source:refseq;acc:nm_016101]	Rooted	49.0663	54.4978	1.1107	
320	40s ribosomal protein s29. [source:swissprot;acc:p30054]	Rooted	50.2784	45.294	1.11005	
320	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [source:swissprot;acc:p12830]	Ranked	241.892	265.96	1.0995	
320	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [source:swissprot;acc:p07099]	Squared	87971.9	69563.1	1.26463	
320	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	Measured	20911	24908.5	1.19117	
321	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	Ranked	241.892	265.959	1.09949	

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/