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

Results: HTML CSV LaTeX

Showing element 1501 to 1550 of 77072 in total

Rank	description	Value Type	Network Comparison Type	Interaction Map	Filtered	green	red	network_comparison
47	trs85 homolog. [swissprot;acc:q9y2l5]	Measured	Subtracted	High confidence	1	20431.7	24896.4	4464.7
	tubulin beta-4q chain. [swissprot;acc:q99867]	Squared		Low confidence	0	35039.5	39955.9	4916.4
	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]	Measured		High confidence	0	3118.3	3645.5	527.2
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Squared	Divided	High confidence	1	56927.2	98517.9	1.73059
48	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]	Ranked	Subtracted	Low confidence	1	235.017	259.517	24.5
	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	Squared	Subtracted	High confidence	0	54614.9	49458.1	5156.8
	b24o18.3 (pom121 membrane glycoprotein (rat homolog)-like 2). [sptrembl;acc:q96kw2]	Ranked	Divided	Low confidence		14002.9	10664.4	1.31305
	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Measured	Divided	High confidence		403.196	870.482	2.15895
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		Subtracted			481.725	999.28	517.555
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]		Divided		1	1390.33	779.167	1.78438
	eferin. [swissprot;acc:o75154]		Subtracted	Low confidence		8696.7	7407.56	1289.14
	eferin. [swissprot;acc:o75154]	Rooted				81.4944	73.6221	7.8723
	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	Measured			0	4840.17	5240.94	400.77
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Ranked	Divided	High confidence	1	83.0461	65.4586	1.26868
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Ranked	Subtracted	Low confidence	0	17020.5	13825.5	3195
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Squared	Divided	High confidence		176.164	960.518	5.45241
	importin 9. [refseq;acc:nm_018085]	Rooted	Subtracted			29.828	21.8651	7.9629
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Squared	Divided		1	10703.5	6300.2	1.69891
	latrophilin 2; lectomedin-1; latrophilin homolog 2 (cow). [refseq;acc:nm_012302]	Rooted	Subtracted	Low confidence	0	10.5357	16.1864	5.6507
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Rooted		High confidence	1	120.823	137.446	16.623
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Squared		Low confidence	1	61881.5	82347.8	20466.3
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Rooted	Divided		0	5.80678	9.84765	1.69589
	mstp028 protein. [refseq;acc:nm_031954]	Squared	Subtracted			110835	105962	4873
	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	Ranked	Divided	High confidence		6909	9830	1.42278
	pnas-129. [sptrembl;acc:q9bxv8]	Measured	Divided	Low confidence		151.073	366.666	2.42708
	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	Squared	Subtracted	High confidence	1	136638	210199	73561
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Rooted	Divided	Low confidence		75.3798	66.6504	1.13097
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Ranked	Divided	Low confidence		217.217	242.742	1.11751
	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	Ranked	Subtracted	High confidence	0	14447.8	18359.8	3912
	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Rooted	Divided	High confidence	1	44.0299	27.7254	1.58807
	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	Squared	Divided	Low confidence	0	83.2781	14.8569	5.60535
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Ranked	Subtracted	High confidence	1	290	350	60
	transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9]	Measured	Divided	Low confidence		9645.34	8313.02	1.16027
	trophinin. [swissprot;acc:q12816]	Squared	Divided	Low confidence		61881.5	82347.8	1.33073
	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Measured	Subtracted	High confidence		20369.9	24806.9	4437
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	Rooted	Divided	High confidence	0	9.31487	15.0533	1.61605
49	60s ribosomal protein l18a. [swissprot;acc:q02543]	Squared	Subtracted	Low confidence		26833.6	21978	4855.6
	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]		Subtracted	High confidence		6483.52	11625.2	5141.68
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]		Divided	High confidence	1	17134.8	28994.2	1.69212
	bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8]	Ranked		Low confidence	0	11141.9	14607.1	1.31101
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]			High confidence	1	105	133	1.26667
	brain protein 16. [refseq;acc:nm_016458]				0	4854.99	6890.54	1.41927
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Measured	Subtracted		1	20369.9	24806.9	4437
	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	Squared				131906	201896	69990
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Rooted		Low confidence		56.7071	48.8531	7.854
	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Ranked		High confidence		290	350	60
	dead-box protein. [refseq;acc:nm_018665]	Ranked		High confidence	0	14486	10628.3	3857.7
	dj254p11.1 (novel protein similar to rna polymerase ii elongation factor siii, subunit p15). [sptrembl;acc:q9h575]	Rooted		Low confidence		9.094	14.7386	5.6446
	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	Squared	Divided	High confidence		43.7473	8.10857	5.39519
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Measured	Subtracted	High confidence		662	153	509

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/