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

Results: HTML CSV LaTeX

Showing element 3180 to 3229 of 38536 in total

Network Comparison Type

: Divided

network_comparison	green	Filtered	description	Interaction Map	Value Type	Rank	red
1.004	213.574	1	mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [swissprot;acc:o15198]	High confidence	Ranked	2381	212.724
	213.574		thioredoxin, mitochondrial precursor (mt-trx) (thioredoxin 2). [swissprot;acc:q99757]	High confidence	Ranked	2383	212.724
	8816.94		helix-loop-helix protein 1 (hen1) (nescient helix loop helix 1) (nscl- 1). [swissprot;acc:q02575]	Low confidence	Measured	4952	8852.22
1.00401	68.1519		ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]		Rooted	4983	67.8798
1.00401	203.803		neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]		Ranked	4812	202.989
1.00402	219.434		26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	High confidence		2368	218.555
			adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186]			2369
			rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]			2371
			ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5]			2370
	10637.6	0	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	Low confidence		810	10680.4
1.00403	66.6337	1	pap-1 binding protein. [refseq;acc:nm_031288]		Rooted	4982	66.3661
	11720.2	0	histone h4. [swissprot;acc:p02304]		Ranked	809	11673.1
	47156.9	1	cerebral cell adhesion molecule. [refseq;acc:nm_016174]		Squared	4950	47346.8
1.00405	8817.96	1	pth-responsive osteosarcoma b1 protein. [refseq;acc:nm_014451]		Measured	4951	8853.63
1.00406	10646.1	0	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]		Ranked	808	10603
1.00407	202.529	1	14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	High confidence		2366	203.353
1.00407	218.475	1	26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231]			2367	217.589
1.00408	198.708	0	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]		Rooted	481	197.901
	198.708	0		Low confidence	Rooted	804	197.901
	203.394	1	transcription factor-like protein 4 (max-like bhlhzip protein) (bigmax protein) (mlx). [swissprot;acc:q9uh92]		Ranked	4811	204.224
	8165.74	0	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		Ranked	807	8132.58
1.00409	22.8556	0	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]		Rooted	803	22.949
1.0041	8819.28	1	helix-loop-helix protein 2 (hen2) (nescient helix loop helix 2) (nscl- 2). [swissprot;acc:q02577]		Measured	4950	8855.48
1.00411	21880	0	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	High confidence	Ranked	491	21970
1.00412	8920.14	1	lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571]	Low confidence	Measured	4949	8883.53
1.00412	41169.4		guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]		Squared	4949	41339.1
1.00413	68.8242		aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]		Rooted	4981	68.5409
1.00413	209.82		glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2]	High confidence	Ranked	2365	208.958
1.00414	213.697		transaldolase (ec 2.2.1.2). [swissprot;acc:p37837]			2364	212.816
1.00415	208.037		phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558]			2362	207.178
	208.046		alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733]			2363	207.186
			beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]			2361
			gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104]			2360
	208.056		phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205]			2359	207.196
	208.098		putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	Low confidence		4810	207.238
1.00416	203.364		mondoa. [refseq;acc:nm_014938]			4809	204.211
1.00416	47268.9		carboxypeptidase a4 precursor (ec 3.4.17.-) (carboxypeptidase a3). [swissprot;acc:q9ui42]		Squared	4948	47465.6
1.00417	193.119		farnesyl-diphosphate farnesyltransferase (ec 2.5.1.21) (squalene synthetase) (sqs) (ss) (fpp:fpp farnesyltransferase). [swissprot;acc:p37268]		Ranked	4808	192.317
1.00417	193.119		protein c14orf1 (hspc288) (protein ad-011) (x0006). [swissprot;acc:q9ukr5]		Ranked	4807	192.317
1.00418	56.1514		pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618]	High confidence	Rooted	2676	56.3861
1.00419	204.601		mucolipin 1; mucolipidin. [refseq;acc:nm_020533]	Low confidence	Ranked	4806	205.458
1.0042	198.026		programmed cell death 4 isoform 1; programmed cell death 4; nuclear antigen h731. [refseq;acc:nm_014456]			4802	198.857
	201.442		cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129]			4804	202.289
			histone-lysine n-methyltransferase, h3 lysine-79 specific (ec 2.1.1.43) (histone h3-k79 methyltransferase) (h3-k79-hmtase) (dot1-like protein). [swissprot;acc:q8tek3]			4805
			tumor antigen slp-8p. [refseq;acc:nm_016516]			4803
	202.787		yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470]			4801	201.939
	4145.95		trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	High confidence	Measured	2698	4163.36
1.00421	211.108		adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367]	Low confidence	Ranked	4800	210.222
1.00421	1903.96	0	lamin b2. [swissprot;acc:q03252]		Squared	816	1895.97
1.00422	45801.6	1	voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448]		Squared	4947	45994.9

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/