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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 4208 to 4257 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
263	trs85 homolog. [swissprot;acc:q9y2l5]	Measured	Divided	1	24896.4	20431.7	1.21852
264	3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	Measured	Subtracted	0	1837.26	1721.76	115.5
	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	Ranked	Subtracted	1	243.24	266.796	23.556
	60s ribosomal protein l12. [swissprot;acc:p30050]	Squared	Divided	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]		Divided	1	26157.6	20236.2	1.29261
	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]		Subtracted	1	53174	44377.4	8796.6
	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	Divided	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	Divided	1	4987.58	4094.57	1.2181
	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	Measured	Subtracted		12503.3	11212	1291.3
	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	Ranked	Divided		219.421	196.978	1.11394
	ns1-associated protein 1. [refseq;acc:nm_006372]	Rooted	Subtracted		52.7642	61.9019	9.1377
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Rooted		0	17.9668	15.7772	2.1896
	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	Ranked			12783	13698	915
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Measured	Divided		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			11.0015	9.99917	1.10024
	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	Rooted		1	66.1122	74.1438	1.12148
	zinc finger imprinted 2. [swissprot;acc:q9nzv7]	Squared	Subtracted	0	3779	3909.95	130.95
265	40s ribosomal protein s29. [swissprot;acc:p30054]	Rooted	Divided		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
	60s ribosomal protein l9. [swissprot;acc:p32969]	Ranked	Subtracted	1	240.243	263.798	23.555
	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	898
	carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085]	Squared		1	53174	44377.4	8796.6
	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	Ranked	Divided	0	13653.8	14874	1.08937
	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Rooted	Subtracted	1	52.7642	61.9019	9.1377
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Squared	Divided	1	26157.6	20236.2	1.29261
	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	Rooted	Subtracted	0	20.6514	18.5098	2.1416
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Measured		0	0	109	109
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Measured		1	4638.1	5923.4	1285.3
		Ranked	Divided		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
	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]	Squared	Subtracted	0	3778.25	3909.18	130.93
266	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]	Measured	Subtracted		1212.82	1104.61	108.21
	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]		Divided		1475.05	1312.91	1.1235
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]		Divided	1	24806.9	20369.9	1.21782
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Ranked	Subtracted	0	5813.32	6706.32	893
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Squared	Divided	0	3687.33	4640.32	1.25845
	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Rooted	Subtracted	1	52.7702	61.8915	9.1213
	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	Squared	Divided		26157.6	20236.2	1.29261
	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866]	Squared	Subtracted		59335	68062.6	8727.6
	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	Rooted	Divided		66.1064	74.1074	1.12103
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	Ranked	Subtracted		243.12	266.662	23.542
	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	Rooted		0	31.3568	29.2362	2.1206
	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158]	Measured		1	11222.2	9948.93	1273.27
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	Ranked	Divided	0	13483.3	14685.4	1.08915
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Rooted		0	39.5626	36.099	1.09595
	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	Ranked		1	241.07	267.88	1.11121
	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	Squared	Subtracted	0	3778.33	3909.26	130.93
267	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]	Rooted	Subtracted	0	4.30525	2.18581	2.11944

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/