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

Results: HTML CSV LaTeX

Showing element 1323 to 1372 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
166	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Squared	1	173408	242989	1.40126
	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	Squared	0	220.039	350.57	1.59322
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Rooted	1	55.6495	65.1458	1.17064
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Measured	1	23693.7	18263	1.29736
	my016 protein. [sptrembl;acc:q9h3k6]	Ranked	0	5561.19	6366.91	1.14488
	zinc finger imprinted 2. [swissprot;acc:q9nzv7]	Rooted		17.1395	14.7969	1.15832
167	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	Squared		168.446	105.991	1.58925
	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]	Ranked	1	209.299	249.187	1.19058
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Squared		173408	242989	1.40126
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Rooted		55.65	65.1448	1.17062
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Measured		23693.7	18263	1.29736
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Ranked	0	12157.6	13890.3	1.14252
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Rooted		52.8301	45.6332	1.15771
	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]	Measured		331.61	417.983	1.26047
168	fos-related antigen 2. [swissprot;acc:p15408]	Ranked		7091.75	6217.28	1.14065
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Ranked	1	82.5916	98.0548	1.18722
	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	Squared	0	338.863	213.584	1.58656
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Measured	1	23693.7	18263	1.29736
	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	Rooted	0	43.2078	37.3703	1.15621
	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Squared	1	173408	242989	1.40126
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Rooted	1	56.3709	65.8949	1.16895
	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525]	Measured	0	334.012	420.355	1.2585
169	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	Ranked	0	9875.43	11256.8	1.13988
	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Ranked	1	82.5916	98.0548	1.18722
	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	Rooted	1	62.762	53.7761	1.1671
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Measured	0	244	194	1.25773
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Squared		14.0914	8.90793	1.58189
	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	Rooted		6.48074	7.48331	1.1547
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Measured	1	23693.7	18263	1.29736
	symplekin. [swissprot;acc:q92797]	Squared		124118	88668.8	1.39979
170	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	Rooted		53.4993	45.9227	1.16499
	calcyphosine. [swissprot;acc:q13938]	Squared	0	175.528	276.854	1.57726
	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	Squared	1	96730.5	69286.7	1.39609
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Ranked	0	11364	12941	1.13877
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Measured	1	23693.7	18263	1.29736
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Ranked	1	227.199	192.715	1.17894
	serpin b11. [swissprot;acc:q96p15]	Rooted	0	6.48074	7.48331	1.1547
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	Measured	0	112.666	141.702	1.25772
171	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	Squared	1	96602.7	69211.2	1.39577
	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	Rooted	0	6.48074	7.48331	1.1547
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Rooted	1	61.6639	71.7355	1.16333
	lamin b2. [swissprot;acc:q03252]	Ranked	0	12135.4	13802	1.13733
	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]	Measured	1	23693.7	18263	1.29736
	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Ranked	1	227.202	192.823	1.17829
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Squared	0	1592.06	2488.07	1.5628
	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	Measured	0	112.666	141.702	1.25772
172	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Ranked	1	174.667	205.556	1.17685
	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	Squared	1	121579	87259.3	1.39331
	likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]	Squared	0	47.4746	74.0536	1.55986
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Rooted	0	40.4536	35.073	1.15341

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/