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 1675 to 1724 of 25824 in total 
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
210	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	Ranked	Divided	285.684	252.234	1.13261	
210	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Rooted	Subtracted	121.695	131.815	10.12	
210	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Measured	Subtracted	4355.61	5810.82	1455.21	
210	rna-binding protein. [source:refseq;acc:nm_019027]	Ranked	Subtracted	237.302	212.41	24.892	
210	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [source:swissprot;acc:o43765]	Squared	Divided	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	Divided	4068.82	5082.21	1.24906	
211	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	Ranked	Subtracted	237.302	212.41	24.892	
211	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	Squared	Subtracted	28994.2	17134.8	11859.4	
211	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Rooted	Subtracted	121.695	131.815	10.12	
211	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Measured	Subtracted	4358.13	5811.49	1453.36	
211	metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm_014889]	Rooted	Divided	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	Divided	14668.3	19547	1.3326	
211	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	Ranked	Divided	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	Divided	4068.91	5082.27	1.24905	
212	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	Rooted	Divided	88.4266	77.5047	1.14092	
212	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	Ranked	Divided	285.684	252.234	1.13261	
212	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Rooted	Subtracted	121.695	131.815	10.12	
212	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Ranked	Subtracted	237.302	212.41	24.892	
212	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	Squared	Divided	14690.3	19560.2	1.3315	
212	putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm_014453]	Squared	Subtracted	28994.2	17134.8	11859.4	
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	Divided	4446.72	5553.79	1.24896	
212	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Measured	Subtracted	6416.68	7865.15	1448.47	
213	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	Rooted	Divided	105.205	92.2415	1.14054	
213	associated molecule with the sh3 domain of stam. [source:refseq;acc:nm_006463]	Squared	Subtracted	28994.2	17134.8	11859.4	
213	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	Measured	Subtracted	7711.38	6265.8	1445.58	
213	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Ranked	Subtracted	237.302	212.41	24.892	
213	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	Rooted	Subtracted	121.695	131.815	10.12	
213	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	Measured	Divided	4446.72	5553.79	1.24896	
213	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	Ranked	Divided	210.693	186.95	1.127	
213	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [source:refseq;acc:nm_003473]	Squared	Divided	86861.5	65369.7	1.32877	
214	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Rooted	Subtracted	121.695	131.815	10.12	
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	Ranked	Divided	191.644	170.192	1.12605	
214	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	Measured	Subtracted	7711.36	6265.79	1445.57	
214	mitochondrial ribosomal protein l4 isoform a. [source:refseq;acc:nm_015956]	Ranked	Subtracted	241.282	266.12	24.838	
214	neuroendocrine differentiation factor; comparative gene identification transcript 149. [source:refseq;acc:nm_016079]	Squared	Subtracted	28994.2	17134.8	11859.4	
214	putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm_014453]	Rooted	Divided	105.205	92.2415	1.14054	
214	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	Squared	Divided	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	Divided	4074.83	5086.49	1.24827	
215	associated molecule with the sh3 domain of stam. [source:refseq;acc:nm_006463]	Rooted	Divided	105.205	92.2415	1.14054	
215	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Ranked	Subtracted	237.292	212.457	24.835	
215	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Rooted	Subtracted	121.695	131.815	10.12	
215	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Ranked	Divided	112	126	1.125	
215	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [source:refseq;acc:nm_001872]	Measured	Subtracted	7711.31	6265.76	1445.55	
215	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Squared	Subtracted	28994.2	17134.8	11859.4	
215	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [source:swissprot;acc:p24723]	Squared	Divided	86609.4	65234.5	1.32766	
215	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [source:swissprot;acc:p01116]	Measured	Divided	16074	12888.4	1.24717	
216	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [source:swissprot;acc:p30084]	Measured	Subtracted	10067.9	11511	1443.1	
216	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Rooted	Subtracted	121.695	131.815	10.12	
216	j kappa-recombination signal binding protein (rbp-j kappa). [source:swissprot;acc:q06330]	Squared	Subtracted	46785.7	58383.2	11597.5	
216	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [source:swissprot;acc:q9uq13]	Measured	Divided	16071.6	12886.8	1.24714	

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/