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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 825 to 874 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
207	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	Rooted	140.508	122.878	1.14348	
207	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [source:swissprot;acc:p49810]	Ranked	285.684	252.234	1.13261	
207	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [source:refseq;acc:nm_018158]	Squared	70525.9	52678.7	1.33879	
207	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	Measured	4771.21	5961.43	1.24946	
208	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	Rooted	46.901	53.624	1.14334	
208	cyclin-dependent kinases regulatory subunit 2 (cks-2). [source:swissprot;acc:p33552]	Squared	70525.9	52678.7	1.33879	
208	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [source:swissprot;acc:p34991]	Ranked	285.684	252.234	1.13261	
208	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [source:swissprot;acc:q8wxs5]	Measured	4068.78	5082.18	1.24907	
209	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [source:swissprot;acc:p17655]	Rooted	46.8525	53.5324	1.14257	
209	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [source:refseq;acc:nm_003798]	Squared	70525.9	52678.7	1.33879	
209	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [source:refseq;acc:nm_018315]	Ranked	285.684	252.234	1.13261	
209	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [source:swissprot;acc:o60359]	Measured	4068.78	5082.18	1.24907	
210	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [source:swissprot;acc:p07384]	Rooted	46.8525	53.5316	1.14256	
210	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	Ranked	285.684	252.234	1.13261	
210	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [source:swissprot;acc:o43765]	Squared	69549	92953.5	1.33652	
210	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [source:swissprot;acc:q9y698]	Measured	4068.82	5082.21	1.24906	
211	metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm_014889]	Rooted	88.4361	77.5112	1.14095	
211	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Squared	14668.3	19547	1.3326	
211	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	Ranked	285.684	252.234	1.13261	
211	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [source:swissprot;acc:q9ubn1]	Measured	4068.91	5082.27	1.24905	
212	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	Rooted	88.4266	77.5047	1.14092	
212	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	Ranked	285.684	252.234	1.13261	
212	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	Squared	14690.3	19560.2	1.3315	
212	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [source:swissprot;acc:q92994]	Measured	4446.72	5553.79	1.24896	
213	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	Rooted	105.205	92.2415	1.14054	
213	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	Measured	4446.72	5553.79	1.24896	
213	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	Ranked	210.693	186.95	1.127	
213	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [source:refseq;acc:nm_003473]	Squared	86861.5	65369.7	1.32877	
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	Ranked	191.644	170.192	1.12605	
214	putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm_014453]	Rooted	105.205	92.2415	1.14054	
214	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	Squared	52591.3	69845.1	1.32807	
214	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	Measured	4074.83	5086.49	1.24827	
215	associated molecule with the sh3 domain of stam. [source:refseq;acc:nm_006463]	Rooted	105.205	92.2415	1.14054	
215	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Ranked	112	126	1.125	
215	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [source:swissprot;acc:p24723]	Squared	86609.4	65234.5	1.32766	
215	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [source:swissprot;acc:p01116]	Measured	16074	12888.4	1.24717	
216	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [source:swissprot;acc:q9uq13]	Measured	16071.6	12886.8	1.24714	
216	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Ranked	112	126	1.125	
216	neuroendocrine differentiation factor; comparative gene identification transcript 149. [source:refseq;acc:nm_016079]	Rooted	105.205	92.2415	1.14054	
216	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [source:swissprot;acc:q02156]	Squared	86600.9	65229.9	1.32763	
217	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Ranked	112	126	1.125	
217	peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [source:swissprot;acc:p23284]	Squared	86600.9	65229.9	1.32763	
217	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Rooted	105.205	92.2415	1.14054	
217	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [source:swissprot;acc:o15211]	Measured	16071.6	12886.8	1.24714	
218	hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	Rooted	46.1476	52.5742	1.13926	
218	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Ranked	112	126	1.125	
218	transforming protein p21/h-ras-1 (c-h-ras). [source:swissprot;acc:p01112]	Measured	16070.4	12886	1.24712	
218	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [source:swissprot;acc:o15294]	Squared	86600.9	65229.9	1.32763	
219	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [source:swissprot;acc:p13073]	Squared	86600.9	65229.9	1.32763	
219	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	Rooted	52.7146	60.0088	1.13837	

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/