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 583 to 632 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
583	opsin 4 (melanopsin). [source:swissprot;acc:q9uhm6]	237.28	252.492	1.06411	
584	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [source:swissprot;acc:o43763]	237.28	252.492	1.06411	
585	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [source:swissprot;acc:p31314]	237.28	252.492	1.06411	
586	hect domain containing protein 1 (fragment). [source:swissprot;acc:q9ult8]	237.28	252.492	1.06411	
587	homeobox protein barh-like 2. [source:swissprot;acc:q9umq3]	237.28	252.492	1.06411	
588	shwachman-bodian-diamond syndrome protein (cgi-97). [source:swissprot;acc:q9y3a5]	216.557	230.362	1.06375	
589	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [source:swissprot;acc:q9y333]	228.215	214.546	1.06371	
590	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	217.215	204.279	1.06333	
591	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [source:swissprot;acc:p78346]	216.72	230.439	1.0633	
592	protein phosphatase 1, regulatory subunit 7; sds22. [source:refseq;acc:nm_002712]	91.63	97.4011	1.06298	
593	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [source:swissprot;acc:q01658]	232.118	218.406	1.06278	
594	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [source:swissprot;acc:o60508]	223.282	210.136	1.06256	
595	vav proto-oncogene. [source:swissprot;acc:p15498]	212.2	199.849	1.0618	
596	vav-3 protein. [source:swissprot;acc:q9ukw4]	212.253	199.908	1.06175	
597	vav-2 protein. [source:swissprot;acc:p52735]	212.526	200.212	1.0615	
598	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [source:swissprot;acc:p31749]	248.463	234.095	1.06138	
599	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]	248.463	234.095	1.06138	
600	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]	248.463	234.095	1.06138	
601	vam6/vps39-like protein (hvam6p). [source:swissprot;acc:q96jc1]	206.274	218.792	1.06069	
602	microtubule-associated protein 4 (map 4). [source:swissprot;acc:p27816]	206.274	218.792	1.06069	
603	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [source:swissprot;acc:q9uju2]	225.829	212.945	1.0605	
604	60s ribosomal protein l15. [source:swissprot;acc:p39030]	217.862	230.978	1.0602	
605	histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	247.47	233.441	1.0601	
606	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	247.47	233.441	1.0601	
607	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]	247.47	233.441	1.0601	
608	histone h2b. [source:refseq;acc:nm_175055]	247.47	233.441	1.0601	
609	histone h2b.s (h2b/s). [source:swissprot;acc:p57053]	247.47	233.441	1.0601	
610	histone h2b.d (h2b/d). [source:swissprot;acc:q99877]	247.47	233.441	1.0601	
611	histone h3.4 (h3t) (h3/t) (h3/g). [source:swissprot;acc:q16695]	247.47	233.441	1.0601	
612	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [source:refseq;acc:nm_170610]	247.47	233.441	1.0601	
613	histone h2b.e (h2b/e). [source:swissprot;acc:q99879]	247.47	233.441	1.0601	
614	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [source:swissprot;acc:p31260]	214.257	202.125	1.06002	
615	homeobox protein hox-b9 (hox-2e) (hox-2.5). [source:swissprot;acc:p17482]	214.257	202.132	1.05999	
616	homeobox protein hox-a9 (hox-1g). [source:swissprot;acc:p31269]	214.257	202.132	1.05999	
617	homeobox protein hox-c9 (hox-3b). [source:swissprot;acc:p31274]	214.257	202.135	1.05997	
618	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	214.256	202.139	1.05994	
619	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [source:swissprot;acc:q14488]	214.256	202.139	1.05994	
620	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q8n1c3]	214.256	202.14	1.05994	
621	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p47869]	214.256	202.14	1.05994	
622	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q16445]	214.256	202.14	1.05994	
623	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p18507]	214.256	202.14	1.05994	
624	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [source:refseq;acc:nm_016123]	214.256	202.139	1.05994	
625	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p48169]	214.256	202.14	1.05994	
626	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [source:swissprot;acc:p78334]	214.256	202.14	1.05994	
627	phosphatidylserine receptor; phosphatidylserine receptor beta. [source:refseq;acc:nm_015167]	214.256	202.139	1.05994	
628	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	214.256	202.14	1.05994	
629	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	214.256	202.14	1.05994	
630	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [source:swissprot;acc:p56556]	214.256	202.141	1.05993	
631	similar to expressed sequence aa415817. [source:sptrembl;acc:q8n4q9]	214.256	202.141	1.05993	
632	homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	214.254	202.166	1.05979	

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/