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 2051 to 2100 of 16578 in total 
Value Type	Ranked
Filtered	1

Rank	Hugo	description	Network Comparison Type	Interaction Map	red	green	network_comparison	
513	DVL1	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	Divided	High confidence	218.596	204.344	1.06975	
513	LSM6	u6 snrna-associated sm-like protein lsm6 (sm protein f). [source:swissprot;acc:q9y4y8]	Subtracted	High confidence	227.483	212.994	14.489	
514	DVL2	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	Divided	High confidence	218.613	204.382	1.06963	
514	FOXO3	forkhead box protein o3a (forkhead in rhabdomyosarcoma-like 1) (af6q21 protein). [source:swissprot;acc:o43524]	Subtracted	Low confidence	205.156	198.715	6.441	
514	HBQ1	hemoglobin theta-1 chain. [source:swissprot;acc:p09105]	Divided	Low confidence	205.157	198.715	1.03242	
514	PLRG1	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	Subtracted	High confidence	222.893	208.523	14.37	
515	AKT1	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [source:swissprot;acc:p31749]	Subtracted	High confidence	248.463	234.095	14.368	
515	APLP2	amyloid-like protein 2 precursor (amyloid protein homolog) (apph) (cdei-box binding protein) (cdebp). [source:swissprot;acc:q06481]	Subtracted	Low confidence	205.156	198.715	6.441	
515	PES1	pescadillo homolog 1. [source:swissprot;acc:o00541]	Divided	High confidence	251.297	234.941	1.06962	
515	TTYH1	tweety homolog 1; tweety homolog. [source:refseq;acc:nm_020659]	Divided	Low confidence	205.156	198.715	1.03241	
516	AKT3	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [source:swissprot;acc:q9y243]	Subtracted	High confidence	248.463	234.095	14.368	
516	CYGB	cytoglobin (histoglobin) (hgb) (stellate cell activation-associated protein). [source:swissprot;acc:q8wwm9]	Divided	Low confidence	205.156	198.715	1.03241	
516	LSM8	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	Divided	High confidence	228.255	213.422	1.0695	
516	SORBS2	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [source:refseq;acc:nm_021069]	Subtracted	Low confidence	205.451	199.011	6.44	
517	AKT2	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [source:swissprot;acc:p31751]	Subtracted	High confidence	248.463	234.095	14.368	
517	FOXO3	forkhead box protein o3a (forkhead in rhabdomyosarcoma-like 1) (af6q21 protein). [source:swissprot;acc:o43524]	Divided	Low confidence	205.156	198.715	1.03241	
517	MTX2	metaxin 2. [source:swissprot;acc:o75431]	Divided	High confidence	219.537	234.793	1.06949	
517	POLI	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	Subtracted	Low confidence	203.167	196.732	6.435	
518	APLP2	amyloid-like protein 2 precursor (amyloid protein homolog) (apph) (cdei-box binding protein) (cdebp). [source:swissprot;acc:q06481]	Divided	Low confidence	205.156	198.715	1.03241	
518	DVL1	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	Subtracted	High confidence	218.596	204.344	14.252	
518	GNL3	nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366]	Divided	High confidence	250.858	234.563	1.06947	
518	MEGF11	megf11 protein. [source:refseq;acc:nm_032445]	Subtracted	Low confidence	207.951	201.517	6.434	
519	DVL2	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	Subtracted	High confidence	218.613	204.382	14.231	
519	DVL3	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	Divided	High confidence	218.702	204.582	1.06902	
519	SAMSN1	sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [source:swissprot;acc:q9nsi8]	Divided	Low confidence	204.278	210.893	1.03238	
519	SLC2A11	solute carrier family 2, facilitated glucose transporter, member 11 (glucose transporter type 11) (glucose transporter type 10). [source:swissprot;acc:q9byw1]	Subtracted	Low confidence	205.551	199.117	6.434	
520	GYG1	glycogenin-1 (ec 2.4.1.186). [source:swissprot;acc:p46976]	Divided	Low confidence	200.014	193.745	1.03236	
520	MEGF10	megf10 protein. [source:refseq;acc:nm_032446]	Subtracted	Low confidence	207.949	201.517	6.432	
520	PRPF19	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	Subtracted	High confidence	223.356	209.149	14.207	
520	SLC35D2	sqv-7-like protein (fragment). [source:sptrembl;acc:o95454]	Divided	High confidence	214.754	229.565	1.06897	
521	DVL3	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	Subtracted	High confidence	218.702	204.582	14.12	
521	EXOSC4	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [source:swissprot;acc:q9npd3]	Divided	High confidence	215.237	230.07	1.06891	
521	SLC2A5	solute carrier family 2, facilitated glucose transporter, member 5 (glucose transporter type 5, small intestine) (fructose transporter). [source:swissprot;acc:p22732]	Subtracted	Low confidence	205.548	199.116	6.432	
521	SORBS2	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [source:refseq;acc:nm_021069]	Divided	Low confidence	205.451	199.011	1.03236	
522	PLRG1	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	Divided	High confidence	222.893	208.523	1.06891	
522	SASH1	sam and sh3 domain containing 1. [source:refseq;acc:nm_015278]	Divided	Low confidence	204.276	210.886	1.03236	
522	SFRS11	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [source:swissprot;acc:q05519]	Subtracted	High confidence	229.709	215.631	14.078	
522	SLC2A9	solute carrier family 2, facilitated glucose transporter, member 9 (glucose transporter type 9). [source:swissprot;acc:q9nrm0]	Subtracted	Low confidence	205.549	199.117	6.432	
523	EXOSC2	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [source:swissprot;acc:q13868]	Divided	High confidence	215.237	230.07	1.06891	
523	HIST1H2BL	histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	Subtracted	High confidence	247.47	233.441	14.029	
523	RNF7	ring finger protein 7; sensitive to apoptosis gene. [source:refseq;acc:nm_014245]	Divided	Low confidence	203.162	196.796	1.03235	
523	SLC2A2	solute carrier family 2, facilitated glucose transporter, member 2 (glucose transporter type 2, liver). [source:swissprot;acc:p11168]	Subtracted	Low confidence	205.543	199.115	6.428	
524	AP2M1	clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [source:swissprot;acc:p20172]	Subtracted	Low confidence	211.788	218.216	6.428	
524	EXOSC3	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [source:swissprot;acc:q9nqt5]	Divided	High confidence	215.237	230.07	1.06891	
524	HIST2H2BA	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	Subtracted	High confidence	247.47	233.441	14.029	
524	SLC2A11	solute carrier family 2, facilitated glucose transporter, member 11 (glucose transporter type 11) (glucose transporter type 10). [source:swissprot;acc:q9byw1]	Divided	Low confidence	205.551	199.117	1.03231	
525		histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	Subtracted	High confidence	247.47	233.441	14.029	
525		solute carrier family 2, facilitated glucose transporter, member 3 (glucose transporter type 3, brain). [source:swissprot;acc:p11169]	Subtracted	Low confidence	205.541	199.114	6.427	
525	EXOSC5	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [source:swissprot;acc:q9nqt4]	Divided	High confidence	215.237	230.07	1.06891	
525	SLC2A5	solute carrier family 2, facilitated glucose transporter, member 5 (glucose transporter type 5, small intestine) (fructose transporter). [source:swissprot;acc:p22732]	Divided	Low confidence	205.548	199.116	1.0323	

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/