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 2462 to 2511 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1231	sfrs protein kinase 1; sr protein kinase 1. [source:refseq;acc:nm_003137]	Subtracted	5894.47	6383.73	489.26	
1232	nuclear factor, interleukin 3 regulated. [source:refseq;acc:nm_005384]	Divided	5869.24	6367.8	1.08494	
1232	xap-5 protein (hxc-26 protein). [source:swissprot;acc:q14320]	Subtracted	5894.47	6383.73	489.26	
1233	midasin (midas-containing protein). [source:swissprot;acc:q9nu22]	Subtracted	4483.08	4971.62	488.54	
1233	tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [source:swissprot;acc:p14679]	Divided	6004.54	6514.24	1.08489	
1234	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [source:swissprot;acc:o14737]	Subtracted	4749.52	5237.77	488.25	
1234	similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [source:refseq;acc:nm_145245]	Divided	5807.83	6300.47	1.08482	
1235	ecotropic viral integration site 5; neuroblastoma stage 4s gene. [source:refseq;acc:nm_005665]	Divided	5807.83	6300.47	1.08482	
1235	p47 protein isoform a. [source:refseq;acc:nm_016143]	Subtracted	6444.4	6932.39	487.99	
1236	p10-binding protein. [source:refseq;acc:nm_024491]	Divided	5594.18	6067.49	1.08461	
1236	presenilins associated rhomboid-like protein. [source:refseq;acc:nm_018622]	Subtracted	6153.36	6640.77	487.41	
1237	gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [source:swissprot;acc:o75936]	Subtracted	6153.36	6640.77	487.41	
1237	tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [source:swissprot;acc:q9y3q8]	Divided	5873.56	6370.31	1.08457	
1238	potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [source:swissprot;acc:p98196]	Subtracted	6153.36	6640.77	487.41	
1238	sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [source:refseq;acc:nm_003676]	Divided	5873.56	6370.31	1.08457	
1239	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	Divided	5654.53	6132.76	1.08457	
1239	kccr13l. [source:refseq;acc:nm_139179]	Subtracted	5538.8	6025.51	486.71	
1240	dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [source:swissprot;acc:q06609]	Subtracted	5538.8	6025.51	486.71	
1240	retinoic acid induced 17; pias-like protein hzimp10. [source:refseq;acc:nm_020338]	Divided	5654.54	6132.69	1.08456	
1241	26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [source:swissprot;acc:q13200]	Divided	6436.19	6980.13	1.08451	
1241	serologically defined colon cancer antigen 16. [source:refseq;acc:nm_006649]	Subtracted	6268.94	6755.57	486.63	
1242	delta-interacting protein a (hepatitis delta antigen interacting protein a). [source:swissprot;acc:q15834]	Subtracted	6274.62	6760.78	486.16	
1242	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [source:swissprot;acc:p51965]	Divided	11143.5	10276.3	1.08439	
1243	phafin 2; ph and fyve domain-containing protein 2. [source:refseq;acc:nm_024613]	Subtracted	5885	6371.14	486.14	
1243	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [source:refseq;acc:nm_006357]	Divided	11143.5	10276.3	1.08439	
1244	3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [source:swissprot;acc:p18405]	Subtracted	5885	6371.14	486.14	
1244	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [source:refseq;acc:nm_016538]	Divided	4835.55	5243.23	1.08431	
1245	3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [source:swissprot;acc:p31213]	Subtracted	5885	6371.14	486.14	
1245	casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [source:swissprot;acc:p13862]	Divided	4835.55	5243.23	1.08431	
1246	methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [source:swissprot;acc:q96dp5]	Subtracted	5110.6	5596.73	486.13	
1246	p53-related protein kinase (ec 2.7.1.-) (nori-2). [source:swissprot;acc:q96s44]	Divided	5346.11	5796.72	1.08429	
1247	kinesin protein. [source:refseq;acc:nm_032559]	Subtracted	5356.23	5842.15	485.92	
1247	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [source:swissprot;acc:p18031]	Divided	6278.76	6807.51	1.08421	
1248	ny-ren-62 antigen (fragment). [source:sptrembl;acc:q9y590]	Subtracted	5358.18	5843.73	485.55	
1248	protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [source:swissprot;acc:p17706]	Divided	6275.86	6803.95	1.08415	
1249	kinesin-like protein kif2 (kinesin-2) (hk2). [source:swissprot;acc:o00139]	Subtracted	5359.72	5844.97	485.25	
1249	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [source:refseq;acc:nm_014317]	Divided	4413.55	4784.6	1.08407	
1250	caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [source:swissprot;acc:o75844]	Subtracted	4970.21	5455.34	485.13	
1250	huntingtin interacting protein 1 (hip-i). [source:swissprot;acc:o00291]	Divided	10733.4	9902.6	1.0839	
1251	dystrobrevin binding protein 1; dysbindin. [source:refseq;acc:nm_032122]	Subtracted	5678.02	6161.65	483.63	
1251	regulator of chromosome condensation (cell cycle regulatory protein). [source:swissprot;acc:p18754]	Divided	8618.32	9340.98	1.08385	
1252	metaxin 2. [source:swissprot;acc:o75431]	Subtracted	7033.72	7516.77	483.05	
1252	zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [source:swissprot;acc:o60315]	Divided	8618.32	9340.98	1.08385	
1253	ribokinase (ec 2.7.1.15). [source:swissprot;acc:q9h477]	Subtracted	6210.51	6693.49	482.98	
1253	transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [source:swissprot;acc:p37275]	Divided	8618.32	9340.98	1.08385	
1254	delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [source:swissprot;acc:p13716]	Subtracted	5489.18	5972.09	482.91	
1254	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [source:swissprot;acc:q9y5p4]	Divided	10725.6	9896.32	1.0838	
1255	dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [source:swissprot;acc:p52564]	Subtracted	6105.23	6587.88	482.65	
1255	serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [source:swissprot;acc:p33172]	Divided	5438.66	5893.87	1.0837	
1256	dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [source:swissprot;acc:p46734]	Subtracted	6104.11	6586.48	482.37	

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/