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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2501 to 2550 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
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	
314	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [source:swissprot;acc:p53582]	Ranked	1	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	1	95.0526	85.3206	1.11406	
314	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	Squared	0	6027.87	7086.08	1.17555	
314	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	Measured	1	21632.5	18090	1.19583	
314	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	Measured	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). [source:swissprot;acc:p08865]	Measured	0	1212.82	1104.61	1.09796	
315	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). [source:swissprot;acc:q9y6q5]	Rooted	0	17.9172	16.833	1.06441	
315	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [source:refseq;acc:nm_004712]	Squared	0	36059.4	30745.3	1.17284	
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	1	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	1	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	1	71576.8	56326.7	1.27074	
315	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	Ranked	0	12121.6	12887.6	1.06319	
315	ribosome biogenesis regulatory protein homolog. [source: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). [source:swissprot;acc:o75832]	Squared	0	8620.27	7355.46	1.17196	
316	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [source:swissprot;acc:p16870]	Measured	0	525	576	1.09714	
316	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [source:sptrembl;acc:q9ugb5]	Ranked	0	10768.5	11444	1.06273	
316	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Rooted	1	95.0526	85.3206	1.11406	
316	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Squared	1	28918.3	36746	1.27068	
316	protein translation factor sui1 homolog (sui1iso1). [source:swissprot;acc:p41567]	Ranked	1	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	1	21370.8	17896.5	1.19413	
316	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [source:swissprot;acc:q9upy6]	Rooted	0	41.4068	38.9073	1.06424	
317	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Measured	1	3153.1	3762.56	1.19329	
317	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	Rooted	1	95.0526	85.3206	1.11406	
317	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:q14409]	Rooted	0	7.79521	7.32908	1.0636	
317	lifeguard; kiaa0950 protein. [source:refseq;acc:nm_012306]	Squared	0	237.082	277.442	1.17024	
317	my016 protein. [source:sptrembl;acc:q9h3k6]	Measured	0	1770.21	1615.47	1.09579	
317	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [source:swissprot;acc:q13232]	Squared	1	33982.3	43159.1	1.27005	
317	protein transport protein sec24c (sec24-related protein c). [source:swissprot;acc:p53992]	Ranked	0	19939	18778	1.06183	
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	1	224.445	204.044	1.09998	
318	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:p32189]	Rooted	0	7.80086	7.3344	1.0636	
318	mitochondrial 60s ribosomal protein l3 (l3mt). [source:swissprot;acc:p09001]	Ranked	1	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	1	46739.9	59134.5	1.26518	
318	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Rooted	1	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	1	34190.9	40795.8	1.19318	
318	protein cgi-147. [source:swissprot;acc:q9y3e5]	Measured	0	8396.12	9192.38	1.09484	
318	transcription factor cp2; transcription factor cp2, alpha globin. [source:refseq;acc:nm_005653]	Squared	0	7372.32	6325.27	1.16553	
318	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [source:swissprot;acc:q9nyl9]	Ranked	0	8918.54	9465.32	1.06131	
319	60s ribosomal protein l19. [source:swissprot;acc:p14118]	Ranked	1	240.73	264.729	1.09969	
319	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	Measured	0	1388.45	1268.19	1.09483	
319	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:q14410]	Rooted	0	7.78379	7.31834	1.0636	
319	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [source:swissprot;acc:p40855]	Squared	1	46739.9	59134.5	1.26518	
319	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	Measured	1	20911	24908.5	1.19117	
319	saccharomyces cerevisiae nip7p homolog. [source:refseq;acc:nm_016101]	Rooted	1	49.0663	54.4978	1.1107	

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/