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 Filtered Value Type Network Comparison Type Interaction Map red network_comparison green

Results: HTML CSV LaTeX

Showing element 951 to 1000 of 33156 in total

Filtered	1
Network Comparison Type	Divided

Rank	description	Value Type	Interaction Map	red	network_comparison	green	
119	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	Rooted	High confidence	50.3247	1.25166	62.9892	
119	ubiquitin-like protein nedd8. [source:swissprot;acc:q15843]	Rooted	Low confidence	67.0736	1.08012	72.4478	
120	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	Squared	Low confidence	58384.8	1.14263	51096.7	
120	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [source:refseq;acc:nm_006339]	Measured	High confidence	5136.78	1.34247	6895.98	
120	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Rooted	High confidence	50.3333	1.25154	62.9942	
120	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Measured	Low confidence	11285.3	1.0937	10318.5	
120	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Squared	High confidence	210199	1.53836	136638	
120	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	Ranked	High confidence	269.278	1.21699	327.709	
120	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	Ranked	Low confidence	203.016	1.0687	189.965	
120	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [source:swissprot;acc:q01094]	Rooted	Low confidence	64.712	1.07988	69.8815	
121	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	Squared	Low confidence	43800.4	1.14188	38358.3	
121	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [source:swissprot;acc:p32929]	Ranked	High confidence	269.254	1.2169	327.655	
121	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Rooted	High confidence	50.339	1.25147	62.9975	
121	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Measured	Low confidence	11285.3	1.0937	10318.5	
121	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	Ranked	Low confidence	203.007	1.06854	189.985	
121	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [source:swissprot;acc:p36873]	Squared	High confidence	199594	1.53509	130021	
121	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Rooted	Low confidence	64.712	1.07988	69.8815	
121	transcription factor jun-b. [source:swissprot;acc:p17275]	Measured	High confidence	5579.18	1.3422	7488.4	
122	c-terminal binding protein 1 (ctbp1). [source:swissprot;acc:q13363]	Squared	Low confidence	82257.5	1.14052	72122.5	
122	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	Squared	High confidence	201896	1.53061	131906	
122	high-mobility group 20a. [source:refseq;acc:nm_018200]	Measured	High confidence	5140.14	1.34112	6893.53	
122	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Measured	Low confidence	11285.3	1.0937	10318.5	
122	nanos (fragment). [source:sptrembl;acc:q8wy41]	Ranked	Low confidence	203.66	1.06785	217.479	
122	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [source:refseq;acc:nm_004980]	Ranked	High confidence	269.248	1.21688	327.642	
122	serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [source:swissprot;acc:p53350]	Rooted	Low confidence	68.1979	1.07896	73.5829	
122	transcription factor jun-d. [source:swissprot;acc:p17535]	Rooted	High confidence	63.636	1.25122	79.6225	
123	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [source:refseq;acc:nm_181844]	Squared	Low confidence	81989.8	1.14016	71910.8	
123	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [source:swissprot;acc:q9ubr2]	Rooted	Low confidence	68.1979	1.07896	73.5829	
123	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Measured	High confidence	24260.3	1.33503	18172.1	
123	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Measured	Low confidence	11285.3	1.0937	10318.5	
123	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Rooted	High confidence	54.6527	1.24375	67.9743	
123	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [source:refseq;acc:nm_004979]	Ranked	High confidence	269.23	1.21681	327.601	
123	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Squared	High confidence	192904	1.52896	126167	
123	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	Ranked	Low confidence	202.96	1.06768	190.094	
124	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [source:swissprot;acc:p41182]	Squared	Low confidence	81993.8	1.14016	71914	
124	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [source:refseq;acc:nm_006339]	Ranked	High confidence	208.52	1.21519	171.595	
124	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Measured	Low confidence	11285.3	1.0937	10318.5	
124	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Measured	High confidence	24255.7	1.33501	18168.9	
124	mouse mammary turmor virus receptor homolog 1. [source:refseq;acc:nm_152832]	Rooted	Low confidence	63.5737	1.07715	68.4785	
124	natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [source:swissprot;acc:p49281]	Ranked	Low confidence	224.763	1.06742	210.566	
124	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	Rooted	High confidence	54.6625	1.24304	67.9477	
124	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	Squared	High confidence	192779	1.52884	126095	
125	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	Ranked	Low confidence	213.243	1.0674	227.616	
125	c-terminal binding protein 2 (ctbp2). [source:swissprot;acc:p56545]	Squared	Low confidence	81761.4	1.13985	71730.2	
125	high-mobility group 20a. [source:refseq;acc:nm_018200]	Ranked	High confidence	208.588	1.21429	171.778	
125	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Measured	Low confidence	11285.3	1.0937	10318.5	
125	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Measured	High confidence	24255.7	1.33501	18168.9	
125	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	Squared	High confidence	189976	1.52616	124480	
125	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	Rooted	High confidence	54.8203	1.23921	67.934	
125	sperm associated antigen 7. [source:refseq;acc:nm_004890]	Rooted	Low confidence	132.137	1.0766	122.736	

Legend:
- Rank is the rank after comparing the two networks
- 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/