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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1901 to 1950 of 16578 in total 
Value Type	Ranked
Filtered	1

Rank	Hugo	description	Network Comparison Type	Interaction Map	red	green	network_comparison	
476	FUCA1	tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [source:swissprot;acc:p04066]	Divided	Low confidence	202.271	195.742	1.03336	
476	KCNA4	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [source:swissprot;acc:p22459]	Divided	High confidence	226.681	210.814	1.07527	
476	KCNA4	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [source:swissprot;acc:p22459]	Subtracted	High confidence	226.681	210.814	15.867	
476	PRRX1	paired mesoderm homeobox protein 1 (prx-1) (paired related homeobox protein 1) (homeobox protein phox1). [source:swissprot;acc:p54821]	Subtracted	Low confidence	194.41	201.036	6.626	
477	ARHGEF7	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [source:swissprot;acc:q14155]	Subtracted	High confidence	220.183	236.015	15.832	
477	HNRNPR	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Divided	Low confidence	203.823	197.249	1.03333	
477	NIP7	saccharomyces cerevisiae nip7p homolog. [source:refseq;acc:nm_016101]	Divided	High confidence	251.926	234.547	1.0741	
477	SAMSN1	sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [source:swissprot;acc:q9nsi8]	Subtracted	Low confidence	204.278	210.893	6.615	
478	BLVRB	flavin reductase (ec 1.5.1.30) (fr) (nadph-dependent diaphorase) (nadph-flavin reductase) (flr) (biliverdin reductase b) (ec 1.3.1.24) (bvr-b) (biliverdin-ix beta-reductase) (green heme binding protein) (ghbp). [source:swissprot;acc:p30043]	Divided	Low confidence	207.68	214.591	1.03328	
478	BRF1	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]	Divided	High confidence	228.051	212.321	1.07409	
478	PAK2	serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [source:swissprot;acc:q13177]	Subtracted	High confidence	220.171	235.979	15.808	
478	SASH1	sam and sh3 domain containing 1. [source:refseq;acc:nm_015278]	Subtracted	Low confidence	204.276	210.886	6.61	
479	ARRB2	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Subtracted	Low confidence	194.137	187.552	6.585	
479	COG5	conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [source:swissprot;acc:q9up83]	Subtracted	High confidence	220.172	235.98	15.808	
479	NOLA1	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	Divided	High confidence	228.051	212.321	1.07409	
479	VTA1	protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [source:swissprot;acc:q9np79]	Divided	Low confidence	207.68	214.591	1.03328	
480	C15orf15	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [source:refseq;acc:nm_016304]	Subtracted	Low confidence	206.763	200.18	6.583	
480	NETO2	neuropilin- and tolloid-like protein 2 precursor. [source:refseq;acc:nm_018092]	Divided	High confidence	237.109	254.667	1.07405	
480	PAK1	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [source:swissprot;acc:q13153]	Subtracted	High confidence	220.172	235.98	15.808	
480	SYNCRIP	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Divided	Low confidence	203.822	197.259	1.03327	
481	HNRNPR	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Subtracted	Low confidence	203.823	197.249	6.574	
481	NETO1	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [source:refseq;acc:nm_138966]	Divided	High confidence	237.109	254.667	1.07405	
481	PAK3	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [source:swissprot;acc:o75914]	Subtracted	High confidence	220.171	235.979	15.808	
481	RRAGA	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	Divided	Low confidence	171.564	166.045	1.03324	
482	ARHGEF6	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [source:swissprot;acc:q15052]	Subtracted	High confidence	220.161	235.95	15.789	
482	HNRNPU	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [source:swissprot;acc:q00839]	Divided	High confidence	237.109	254.667	1.07405	
482	PLRG1	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	Subtracted	Low confidence	201.847	195.283	6.564	
482	TRIP12	thyroid receptor interacting protein 12 (trip12). [source:swissprot;acc:q14669]	Divided	Low confidence	204.65	198.086	1.03314	
483		rna-binding protein. [source:refseq;acc:nm_019027]	Divided	Low confidence	203.821	197.289	1.03311	
483	BRF1	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]	Subtracted	High confidence	228.051	212.321	15.73	
483	RUNX2	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [source:swissprot;acc:q13950]	Divided	High confidence	237.109	254.667	1.07405	
483	TRIP12	thyroid receptor interacting protein 12 (trip12). [source:swissprot;acc:q14669]	Subtracted	Low confidence	204.65	198.086	6.564	
484		apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	Divided	Low confidence	203.821	197.291	1.0331	
484	HNRPUL1	e1b-55kda-associated protein 5 isoform a. [source:refseq;acc:nm_007040]	Divided	High confidence	237.109	254.667	1.07405	
484	NOLA1	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	Subtracted	High confidence	228.051	212.321	15.73	
484	SYNCRIP	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Subtracted	Low confidence	203.822	197.259	6.563	
485	BRPF1	tubulin tyrosine ligase-like protein hottl (hqp0207). [source:swissprot;acc:q9y4r7]	Divided	Low confidence	205.109	198.551	1.03303	
485	BRPF1	tubulin tyrosine ligase-like protein hottl (hqp0207). [source:swissprot;acc:q9y4r7]	Subtracted	Low confidence	205.109	198.551	6.558	
485	PPM1B	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [source:swissprot;acc:o75688]	Subtracted	High confidence	231.276	215.627	15.649	
485	RPL18	60s ribosomal protein l18. [source:swissprot;acc:q07020]	Divided	High confidence	237.109	254.667	1.07405	
486	CXorf9	chromosome x open reading frame 9; likely ortholog of mouse sh3 gene sly. [source:refseq;acc:nm_018990]	Divided	Low confidence	204.331	211.075	1.03301	
486	EEF1B2	elongation factor 1-beta (ef-1-beta). [source:swissprot;acc:p24534]	Subtracted	Low confidence	206.154	199.596	6.558	
486	EIF6	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [source:swissprot;acc:p56537]	Subtracted	High confidence	248.866	233.287	15.579	
486	MCTS1	mct-1 protein. [source:refseq;acc:nm_014060]	Divided	High confidence	226.313	243.03	1.07387	
487	ARRB1	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Subtracted	Low confidence	194.237	187.689	6.548	
487	C15orf15	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [source:refseq;acc:nm_016304]	Divided	Low confidence	206.763	200.18	1.03289	
487	MDH2	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [source:swissprot;acc:p40926]	Subtracted	High confidence	238.529	254.099	15.57	
487	MRPL22	mitochondrial ribosomal protein l22. [source:refseq;acc:nm_014180]	Divided	High confidence	226.313	243.03	1.07387	
488		gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Subtracted	High confidence	82.5916	98.0548	15.4632	
488	PCNA	proliferating cell nuclear antigen (pcna) (cyclin). [source:swissprot;acc:p12004]	Subtracted	Low confidence	207.84	201.297	6.543	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/