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 Filtered Network Comparison Type Interaction Map red green network_comparison

Results: HTML CSV LaTeX

Showing element 1551 to 1600 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
194	nuclear protein ukp68. [refseq;acc:nm_024824]	Ranked	1	227.491	199.458	1.14055
194	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	Measured	0	125.5	103.5	1.21256
195	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	Measured		23	19	1.21053
	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Squared		479.423	335.966	1.427
	cyclin g1 (cyclin g). [swissprot;acc:p51959]	Measured	1	17738.5	13995.6	1.26743
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Ranked	1	227.971	200.417	1.13748
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Rooted	0	23.8722	20.933	1.14041
	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]	Rooted	1	59.6399	51.9242	1.1486
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Ranked	0	13942.8	15586.4	1.11788
	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	Squared	1	71062.4	95488.9	1.34373
196	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]		0	479.099	335.74	1.42699
	calsyntenin-1 precursor. [swissprot;acc:o94985]		1	71062.4	95488.9	1.34373
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Ranked		263.215	231.407	1.13745
	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]	Rooted		59.6399	51.9242	1.1486
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Rooted	0	23.8722	20.9332	1.1404
	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]	Measured	1	17738.5	13995.7	1.26742
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Ranked	0	11064.2	9897.84	1.11784
	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	Measured		465.37	562.085	1.20782
197	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Squared		479.099	335.74	1.42699
	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	Measured		2145.97	1784.22	1.20275
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Ranked	1	263.215	231.407	1.13745
	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]	Rooted	1	59.6399	51.9242	1.1486
	importin 4. [refseq;acc:nm_024658]	Ranked	0	12337.6	13788.9	1.11763
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Rooted	0	23.8722	20.9331	1.1404
	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). [swissprot;acc:q15172]	Measured	1	17738.5	13995.7	1.26742
	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). [swissprot;acc:o14521]	Squared		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). [swissprot;acc:p15056]	Measured		17710.9	13977.7	1.26708
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Ranked		263.191	231.394	1.13741
	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]	Rooted		59.6399	51.9242	1.1486
	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	Squared	0	1679.15	1177.18	1.42642
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Rooted	0	23.8722	20.9331	1.1404
	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467]	Squared	1	71062.2	95488.6	1.34373
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	Ranked	0	11781.5	10545.3	1.11723
	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	Measured		247.333	206	1.20065
199	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	Ranked		11781.8	10545.7	1.11721
	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	Measured		1230.54	1026.18	1.19915
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Rooted		23.8722	20.9331	1.1404
	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650]	Squared		21.8736	31.1879	1.42582
	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	Ranked	1	242.735	276.059	1.13729
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Measured		4916.8	3888.18	1.26455
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Rooted		61.2893	70.3856	1.14842
	thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]	Squared		71062.2	95488.6	1.34373
200	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	Measured		4808.79	6074.21	1.26315
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Measured	0	578.056	482.7	1.19755
	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	Ranked	1	242.718	276.018	1.1372
	gk001 protein. [refseq;acc:nm_020198]	Squared	1	71062.2	95488.6	1.34373
	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	Rooted	0	23.8722	20.9333	1.14039
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Rooted	1	61.2893	70.3856	1.14842
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Ranked	0	8786.74	7870.3	1.11644
	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	Squared	0	5317.39	3738.08	1.42249

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/