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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1575 to 1624 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
197	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [source:swissprot;acc:q15172]	Measured	1	17738.5	13995.7	1.26742	
197	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	Squared	1	71062.4	95488.9	1.34373	
198	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [source:swissprot;acc:p15056]	Measured	1	17710.9	13977.7	1.26708	
198	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	Ranked	1	263.191	231.394	1.13741	
198	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	Rooted	1	59.6399	51.9242	1.1486	
198	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [source:swissprot;acc:p15104]	Squared	0	1679.15	1177.18	1.42642	
198	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [source:swissprot;acc:p26371]	Rooted	0	23.8722	20.9331	1.1404	
198	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [source:swissprot;acc:p23467]	Squared	1	71062.2	95488.6	1.34373	
198	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Ranked	0	11781.5	10545.3	1.11723	
198	secreted modular calcium-binding protein 1. [source:refseq;acc:nm_022137]	Measured	0	247.333	206	1.20065	
199	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Ranked	0	11781.8	10545.7	1.11721	
199	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [source:swissprot;acc:p15104]	Measured	0	1230.54	1026.18	1.19915	
199	keratin associated protein 1-3; keratin associated protein 1.3. [source:refseq;acc:nm_030966]	Rooted	0	23.8722	20.9331	1.1404	
199	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [source:refseq;acc:nm_015650]	Squared	0	21.8736	31.1879	1.42582	
199	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [source:swissprot;acc:q9umr5]	Ranked	1	242.735	276.059	1.13729	
199	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [source:swissprot;acc:p05323]	Measured	1	4916.8	3888.18	1.26455	
199	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	Rooted	1	61.2893	70.3856	1.14842	
199	thymus-specific serine protease precursor (ec 3.4.-.-). [source:swissprot;acc:q9nqe7]	Squared	1	71062.2	95488.6	1.34373	
200	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Measured	1	4808.79	6074.21	1.26315	
200	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	Measured	0	578.056	482.7	1.19755	
200	egf-like-domain, multiple 7; neu1 protein. [source:refseq;acc:nm_016215]	Ranked	1	242.718	276.018	1.1372	
200	gk001 protein. [source:refseq;acc:nm_020198]	Squared	1	71062.2	95488.6	1.34373	
200	keratin associated protein 4-10; keratin associated protein 4.10. [source:refseq;acc:nm_033060]	Rooted	0	23.8722	20.9333	1.14039	
200	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Rooted	1	61.2893	70.3856	1.14842	
200	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	Ranked	0	8786.74	7870.3	1.11644	
200	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [source:swissprot;acc:q9y690]	Squared	0	5317.39	3738.08	1.42249	
201	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	Squared	0	351.996	499.177	1.41813	
201	calsyntenin-2 precursor. [source:swissprot;acc:q9h4d0]	Squared	1	71033.4	95440.2	1.3436	
201	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [source:swissprot;acc:p39656]	Rooted	1	61.2893	70.3856	1.14842	
201	keratin associated protein 4-14; keratin associated protein 4.14. [source:refseq;acc:nm_033059]	Rooted	0	23.8722	20.9336	1.14038	
201	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	Ranked	0	16853	15123	1.1144	
201	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	Ranked	1	240.133	211.382	1.13601	
201	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]	Measured	0	6804.88	5690.63	1.1958	
201	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Measured	1	4810.22	6075.04	1.26294	
202	calsyntenin-3 precursor. [source:swissprot;acc:q9bqt9]	Squared	1	71030.1	95434.8	1.34358	
202	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	Measured	0	606.049	723.75	1.19421	
202	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	Squared	0	3339.18	2360.97	1.41433	
202	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	Measured	1	4812.01	6076.09	1.26269	
202	keratin associated protein 4.9 (fragment). [source:sptrembl;acc:q9byq8]	Rooted	0	23.8722	20.9336	1.14038	
202	serpin b11. [source:swissprot;acc:q96p15]	Ranked	0	16853	15123	1.1144	
202	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	Ranked	1	201.478	228.784	1.13553	
202	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	Rooted	1	57.3527	65.7973	1.14724	
203	autophagy protein 12-like (apg12-like). [source:swissprot;acc:o94817]	Measured	1	11757.8	9352.11	1.25723	
203	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	Ranked	0	16853	15123	1.1144	
203	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	Ranked	1	201.515	228.752	1.13516	
203	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	Squared	0	93.5732	66.2405	1.41263	
203	hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	Squared	1	20988.2	15632.1	1.34263	
203	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [source:refseq;acc:nm_015650]	Measured	0	304	363	1.19408	
203	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	Rooted	0	22.1344	25.2414	1.14037	
203	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [source:swissprot;acc:q14186]	Rooted	1	46.3291	53.1063	1.14628	

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/