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 2075 to 2124 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
260	histone h4. [swissprot;acc:p02304]	Squared	0	273623	345123	1.26131
	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	Squared	1	76296.4	58801.6	1.29752
	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	Rooted	1	59.0951	66.4332	1.12417
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	Rooted	0	22.3157	24.6207	1.10329
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Measured	1	4244.95	5193.42	1.22343
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Measured	0	1949.36	2202	1.1296
261	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Ranked		12448.9	11393.9	1.09259
	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	Rooted		22.315	24.6198	1.10328
	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Squared		135280	170628	1.2613
	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Measured		1295.81	1463.55	1.12945
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	Ranked	1	219.421	196.978	1.11394
	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]	Squared		48127.9	62245.6	1.29334
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Rooted		62.3337	70.0738	1.12417
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Measured		4247.36	5192.61	1.22255
262	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	Squared	0	2463.89	3102.4	1.25915
	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Rooted		26.0693	28.761	1.10325
	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	Measured		764.479	676.971	1.12926
	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	Measured	1	24896.4	20431.7	1.21852
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	Ranked		219.421	196.978	1.11394
	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	Squared		26157.6	20236.2	1.29261
	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	Rooted		59.4073	66.7002	1.12276
	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	Ranked	0	3464	3778	1.09065
263	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	Squared	1	26157.6	20236.2	1.29261
	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	Rooted	0	4.79583	4.3589	1.10024
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Ranked	0	13573.3	14801.2	1.09046
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	Ranked	1	219.421	196.978	1.11394
	paxillin. [swissprot;acc:p49023]	Rooted	1	59.4073	66.7002	1.12276
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	Squared	0	2463.98	3102.52	1.25915
	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	Measured	0	1843	1633	1.1286
	trs85 homolog. [swissprot;acc:q9y2l5]	Measured	1	24896.4	20431.7	1.21852
264	60s ribosomal protein l12. [swissprot;acc:p30050]	Squared	0	3686.65	4639.46	1.25845
	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	Squared	1	26157.6	20236.2	1.29261
	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]	Ranked	0	10037.1	10935.1	1.08947
	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	Measured	1	4987.58	4094.57	1.2181
	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	Ranked	1	219.421	196.978	1.11394
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Measured	0	3336.48	2957.12	1.12829
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	Rooted	0	11.0015	9.99917	1.10024
	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]		1	66.1122	74.1438	1.12148
265	40s ribosomal protein s29. [swissprot;acc:p30054]		0	26.1023	28.6733	1.0985
	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Squared		3687.69	4640.77	1.25845
	60s ribosomal protein l9. [swissprot;acc:p32969]	Measured		1685.44	1894.01	1.12375
	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	Ranked		13653.8	14874	1.08937
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Squared	1	26157.6	20236.2	1.29261
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Ranked		225.217	202.459	1.11241
	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	Rooted		56.031	62.8281	1.12131
	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Measured		24806.9	20369.9	1.21782
266	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]		0	1475.05	1312.91	1.1235
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]		1	24806.9	20369.9	1.21782
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Squared	0	3687.33	4640.32	1.25845
	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	Squared	1	26157.6	20236.2	1.29261

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/