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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2151 to 2200 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
269	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	Rooted	1	66.1064	74.1074	1.12103	
269	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	Measured	1	4590.18	5575.52	1.21466	
270	40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Squared	0	2569.37	3201.81	1.24615	
270	crk-like protein. [source:swissprot;acc:p46109]	Rooted	1	66.1064	74.1074	1.12103	
270	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [source:swissprot;acc:q99447]	Ranked	0	10735.1	9891.37	1.0853	
270	fad synthetase. [source:refseq;acc:nm_025207]	Ranked	1	241.373	267.352	1.10763	
270	fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917]	Measured	1	23640.2	19479.8	1.21358	
270	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Measured	0	1217.96	1367.88	1.12309	
270	transcription factor iib. [source:refseq;acc:nm_013242]	Squared	1	64739.9	50300.6	1.28706	
270	zinc finger protein 277. [source:swissprot;acc:q9nrm2]	Rooted	0	90.4079	98.9265	1.09422	
271	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	Ranked	1	241.373	267.352	1.10763	
271	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	Measured	1	2554.89	3093.78	1.21092	
271	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	Squared	0	92.5367	74.2791	1.2458	
271	histone h4. [source:swissprot;acc:p02304]	Measured	0	21773.1	24446.3	1.12278	
271	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [source:refseq;acc:nm_015650]	Rooted	0	17.4356	19.0526	1.09274	
271	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [source:swissprot;acc:p12829]	Ranked	0	10735.1	9891.37	1.0853	
271	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	Rooted	1	66.1064	74.1073	1.12103	
271	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [source:swissprot;acc:q12872]	Squared	1	64739.9	50300.6	1.28706	
272	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Squared	0	4225.7	5255.44	1.24369	
272	60s ribosomal protein l15. [source:swissprot;acc:p39030]	Measured	0	846.216	753.793	1.12261	
272	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [source:swissprot;acc:p10109]	Squared	1	36563.7	46971.1	1.28464	
272	chromodomain y-like protein 2. [source:refseq;acc:nm_152342]	Rooted	0	33.0227	30.2263	1.09252	
272	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Measured	1	3858.52	4669.27	1.21012	
272	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Ranked	1	241.373	267.352	1.10763	
272	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	Rooted	1	66.1064	74.1074	1.12103	
272	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [source:swissprot;acc:q12772]	Ranked	0	7163.55	7759.61	1.08321	
273	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Squared	0	4224.07	5253.37	1.24367	
273	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o43252]	Ranked	1	241.373	267.352	1.10763	
273	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Measured	1	3199.4	3870.8	1.20985	
273	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [source:refseq;acc:nm_001457]	Squared	1	16120.1	20665.7	1.28198	
273	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	Rooted	1	66.1064	74.1074	1.12103	
273	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	Measured	0	1410.81	1582.65	1.1218	
273	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [source:swissprot;acc:o95670]	Rooted	0	24.598	26.8697	1.09235	
273	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [source:swissprot;acc:q9upy6]	Ranked	0	12748.1	11770.9	1.08302	
274	60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	Squared	0	4214.44	5226.4	1.24012	
274	brain protein 16. [source:refseq;acc:nm_016458]	Measured	0	2155.75	2418.14	1.12172	
274	chromosome 3p21.1 gene sequence. [source:refseq;acc:nm_013286]	Measured	1	3119.98	2579.49	1.20953	
274	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	Ranked	0	10432.4	11298.4	1.08301	
274	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [source:swissprot;acc:o75791]	Rooted	1	66.1063	74.1068	1.12102	
274	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Ranked	1	241.373	267.352	1.10763	
274	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Squared	1	16120.1	20665.7	1.28198	
274	testis-specific chromodomain protein y protein 2. [source:swissprot;acc:q9y6f7]	Rooted	0	32.8979	30.1206	1.09221	
275	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Rooted	1	66.1048	74.0977	1.12091	
275	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	Ranked	1	241.373	267.352	1.10763	
275	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	Ranked	0	10783	11674.1	1.08264	
275	pnas-18. [source:sptrembl;acc:q9bzu3]	Squared	0	14643.9	11814.6	1.23947	
275	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Squared	1	16120.1	20665.7	1.28198	
275	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [source:swissprot;acc:p49795]	Measured	1	3119.98	2579.49	1.20953	
275	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. [source:refseq;acc:nm_003075]	Measured	0	717.401	804.725	1.12172	
275	testis-specific chromodomain y protein 1. [source:swissprot;acc:q9y6f8]	Rooted	0	32.8937	30.117	1.0922	

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/