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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1251 to 1300 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
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	
321	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	Squared	33526	42390.2	1.2644	
321	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	Measured	20911	24908.5	1.19117	
321	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Rooted	55.9231	62.0565	1.10968	
322	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	Measured	20911	24908.5	1.19117	
322	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Ranked	86.7483	78.8995	1.09948	
322	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [source:swissprot;acc:p15531]	Squared	33522.8	42384.8	1.26436	
322	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	Rooted	60.594	67.2244	1.10942	
323	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	Ranked	241.884	265.945	1.09947	
323	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	Rooted	50.3803	45.4193	1.10923	
323	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [source:swissprot;acc:p22392]	Squared	33514.4	42370.8	1.26426	
323	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Measured	4620.76	5501.94	1.1907	
324	40s ribosomal protein s23. [source:swissprot;acc:p39028]	Ranked	243.944	268.195	1.09941	
324	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Measured	28136.5	33457.6	1.18912	
324	fad synthetase. [source:refseq;acc:nm_025207]	Rooted	50.3803	45.4193	1.10923	
324	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [source:swissprot;acc:p49590]	Squared	34527.9	43507.9	1.26008	
325	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [source:swissprot;acc:o15235]	Ranked	243.944	268.195	1.09941	
325	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	Rooted	50.3803	45.4193	1.10923	
325	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [source:swissprot;acc:p12081]	Squared	34506.3	43476	1.25994	
325	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	Measured	16177.9	19235.4	1.18899	

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/