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 958 to 1007 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
479	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	1	228.051	212.321	1.07409	
480	neuropilin- and tolloid-like protein 2 precursor. [source:refseq;acc:nm_018092]	1	237.109	254.667	1.07405	
480	uncharacterized bone marrow protein bm033. [source:refseq;acc:nm_018452]	0	15155.8	15031.7	1.00826	
481	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [source:refseq;acc:nm_138966]	1	237.109	254.667	1.07405	
481	uridine kinase-like 1. [source:swissprot;acc:q9nwz5]	0	11554.3	11462.4	1.00802	
482	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [source:swissprot;acc:q00839]	1	237.109	254.667	1.07405	
482	kinesin-like protein kif13b (kinesin-like protein gakin). [source:swissprot;acc:q9nqt8]	0	6156.33	6205.67	1.00801	
483	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [source:swissprot;acc:q13950]	1	237.109	254.667	1.07405	
483	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	0	12223.8	12127.5	1.00794	
484	e1b-55kda-associated protein 5 isoform a. [source:refseq;acc:nm_007040]	1	237.109	254.667	1.07405	
484	protein c20orf45 (cgi-107). [source:swissprot;acc:q9y3b1]	0	11489.7	11414.3	1.00661	
485	60s ribosomal protein l18. [source:swissprot;acc:q07020]	1	237.109	254.667	1.07405	
485	pepsin a precursor (ec 3.4.23.1). [source:swissprot;acc:p00790]	0	12461.5	12542.3	1.00648	
486	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	0	13372.4	13288.3	1.00633	
486	mct-1 protein. [source:refseq;acc:nm_014060]	1	226.313	243.03	1.07387	
487	mitochondrial ribosomal protein l22. [source:refseq;acc:nm_014180]	1	226.313	243.03	1.07387	
487	survival motor neuron protein (component of gems 1) (gemin1). [source:swissprot;acc:q16637]	0	13236.8	13159.3	1.00589	
488	heat shock factor binding protein 1. [source:swissprot;acc:o75506]	0	15204.2	15127.8	1.00505	
488	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]	1	225.026	209.798	1.07258	
489	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	0	8854.04	8811.09	1.00487	
489	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [source:swissprot;acc:o75688]	1	231.276	215.627	1.07257	
490	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [source:swissprot;acc:q9y2s0]	0	10388.7	10338.7	1.00484	
490	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [source:swissprot;acc:q14155]	1	220.183	236.015	1.0719	
491	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [source:swissprot;acc:q9bze4]	1	251.83	234.951	1.07184	
491	rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm_015952]	0	21970	21880	1.00411	
492	serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [source:swissprot;acc:q13177]	1	220.171	235.979	1.0718	
492	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [source:swissprot;acc:q96gm5]	0	6802.96	6829.74	1.00394	
493	conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [source:swissprot;acc:q9up83]	1	220.172	235.98	1.0718	
493	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [source:sptrembl;acc:q9h5b6]	0	11999.1	12041.7	1.00355	
494	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [source:swissprot;acc:q13153]	1	220.172	235.98	1.0718	
494	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [source:swissprot;acc:p08240]	0	11985.5	11959.4	1.00218	
495	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	0	11725.2	11748.1	1.00195	
495	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [source:swissprot;acc:o75914]	1	220.171	235.979	1.0718	
496	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [source:swissprot;acc:q9nq55]	1	250.938	234.134	1.07177	
496	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [source:swissprot;acc:o95670]	0	9394	9411.49	1.00186	
497	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	1	251.344	234.514	1.07177	
497	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm_014633]	0	13692.7	13718.2	1.00186	
498	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	0	10231.8	10248.3	1.00161	
498	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [source:swissprot;acc:q15052]	1	220.161	235.95	1.07172	
499	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [source:swissprot;acc:p12268]	0	9080.73	9069.58	1.00123	
499	triosephosphate isomerase (ec 5.3.1.1) (tim). [source:swissprot;acc:p00938]	1	231.496	248.048	1.0715	
500	huntingtin interacting protein e; huntingtin interactor protein e. [source:refseq;acc:nm_007076]	0	394	394	1	
500	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [source:refseq;acc:nm_001564]	1	224.662	240.673	1.07127	
501	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [source:swissprot;acc:p08574]	1	238.704	255.68	1.07112	
501	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	0	0.00001	0.00001	1	
502	brca1 associated protein. [source:refseq;acc:nm_006768]	0	0.00001	0.00001	1	
502	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	1	238.704	255.68	1.07112	
503	senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	1	238.704	255.68	1.07112	
504	oligophrenin 1. [source:swissprot;acc:o60890]	1	238.704	255.68	1.07112	
505	ad24 protein. [source:refseq;acc:nm_022451]	1	251.334	234.672	1.071	

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/