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 2101 to 2150 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
263	paxillin. [source:swissprot;acc:p49023]	Rooted	1	59.4073	66.7002	1.12276	
263	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Squared	0	2463.98	3102.52	1.25915	
263	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]	Measured	0	1843	1633	1.1286	
263	trs85 homolog. [source:swissprot;acc:q9y2l5]	Measured	1	24896.4	20431.7	1.21852	
264	60s ribosomal protein l12. [source:swissprot;acc:p30050]	Squared	0	3686.65	4639.46	1.25845	
264	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	Squared	1	26157.6	20236.2	1.29261	
264	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [source:swissprot;acc:o43681]	Ranked	0	10037.1	10935.1	1.08947	
264	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Measured	1	4987.58	4094.57	1.2181	
264	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	Ranked	1	219.421	196.978	1.11394	
264	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	Measured	0	3336.48	2957.12	1.12829	
264	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [source:swissprot;acc:p23193]	Rooted	0	11.0015	9.99917	1.10024	
264	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Rooted	1	66.1122	74.1438	1.12148	
265	40s ribosomal protein s29. [source:swissprot;acc:p30054]	Rooted	0	26.1023	28.6733	1.0985	
265	60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Squared	0	3687.69	4640.77	1.25845	
265	60s ribosomal protein l9. [source:swissprot;acc:p32969]	Measured	0	1685.44	1894.01	1.12375	
265	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [source:swissprot;acc:o15488]	Ranked	0	13653.8	14874	1.08937	
265	leucine-rich repeat-containing protein 15 precursor (hlib). [source:swissprot;acc:q8tf66]	Squared	1	26157.6	20236.2	1.29261	
265	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Ranked	1	225.217	202.459	1.11241	
265	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	Rooted	1	56.031	62.8281	1.12131	
265	wd-repeat protein wdc146. [source:swissprot;acc:q9c0j8]	Measured	1	24806.9	20369.9	1.21782	
266	aldehyde dehydrogenase 8 (ec 1.2.1.5). [source:swissprot;acc:p48448]	Measured	0	1475.05	1312.91	1.1235	
266	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	Measured	1	24806.9	20369.9	1.21782	
266	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [source:sptrembl;acc:q9nq02]	Squared	0	3687.33	4640.32	1.25845	
266	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	Squared	1	26157.6	20236.2	1.29261	
266	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Rooted	1	66.1064	74.1074	1.12103	
266	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	Ranked	0	13483.3	14685.4	1.08915	
266	transcription factor cp2; transcription factor cp2, alpha globin. [source:refseq;acc:nm_005653]	Rooted	0	39.5626	36.099	1.09595	
266	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	Ranked	1	241.07	267.88	1.11121	
267	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	Ranked	1	241.07	267.88	1.11121	
267	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	Squared	1	26157.6	20236.2	1.29261	
267	mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [source:swissprot;acc:q99683]	Squared	0	181.291	144.478	1.2548	
267	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	Measured	1	14021.4	11523	1.21682	
267	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [source:swissprot;acc:o60675]	Rooted	0	12.9585	14.1963	1.09552	
267	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [source:swissprot;acc:o00268]	Ranked	0	8054.34	8772.02	1.0891	
267	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Rooted	1	66.1064	74.1073	1.12103	
267	uncharacterized bone marrow protein bm033. [source:refseq;acc:nm_018452]	Measured	0	1475.05	1312.91	1.1235	
268	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	Measured	1	24473.9	20127.8	1.21593	
268	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Ranked	1	271.016	244.167	1.10996	
268	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [source:refseq;acc:nm_003902]	Measured	0	604.529	538.094	1.12346	
268	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	Squared	1	26157.6	20236.2	1.29261	
268	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [source:swissprot;acc:q14168]	Ranked	0	14257.4	13134.5	1.08549	
268	protein cgi-147. [source:swissprot;acc:q9y3e5]	Squared	0	75129.2	94178	1.25355	
268	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Rooted	1	66.1064	74.1074	1.12103	
268	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [source:swissprot;acc:o15525]	Rooted	0	13.0249	14.2577	1.09465	
269	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Measured	0	1217.92	1367.83	1.12309	
269	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Squared	0	4121.56	5159.2	1.25176	
269	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	Ranked	1	241.373	267.352	1.10763	
269	ischemia/reperfusion inducible protein. [source:refseq;acc:nm_024640]	Ranked	0	12463.5	11482.6	1.08542	
269	similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	Rooted	0	90.4079	98.9265	1.09422	
269	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	Squared	1	26157.6	20236.2	1.29261	

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/