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 Value Type description Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 563 to 612 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
563	calcyphosine. [source:swissprot;acc:q13938]	207.121	220.744	1.06577	
564	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	207.121	220.744	1.06577	
565	sedlin. [source:swissprot;acc:o14582]	121.261	129.219	1.06563	
566	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	121.261	129.219	1.06563	
567	bet3 homolog. [source:swissprot;acc:o43617]	121.261	129.219	1.06563	
568	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [source:swissprot;acc:o60231]	212.38	226.3	1.06554	
569	t54 protein. [source:swissprot;acc:q92917]	212.38	226.3	1.06554	
570	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [source:swissprot;acc:q05519]	215.631	229.709	1.06529	
571	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [source:swissprot;acc:p40926]	254.099	238.529	1.06528	
572	cbf1 interacting corepressor. [source:refseq;acc:nm_004882]	213.945	227.86	1.06504	
573	evolutionarily conserved g-patch domain containing. [source:refseq;acc:nm_018025]	213.945	227.86	1.06504	
574	preimplantation protein 3; likely ortholog of preimplantation protein 3. [source:refseq;acc:nm_015387]	208.264	221.807	1.06503	
575	dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [source:swissprot;acc:q9ubs4]	208.264	221.807	1.06503	
576	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [source:sptrembl;acc:q9h5a9]	250.419	235.18	1.0648	
577	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [source:swissprot;acc:p98073]	210.944	224.606	1.06477	
578	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [source:swissprot;acc:q13435]	210.944	224.606	1.06477	
579	zinc finger protein t86. [source:swissprot;acc:o00488]	231.796	246.805	1.06475	
580	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [source:refseq;acc:nm_014596]	252.038	236.751	1.06457	
581	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [source:swissprot;acc:o43711]	252.492	237.28	1.06411	
582	homeobox protein barh-like 1. [source:swissprot;acc:q9hbu1]	252.492	237.28	1.06411	
583	opsin 4 (melanopsin). [source:swissprot;acc:q9uhm6]	252.492	237.28	1.06411	
584	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [source:swissprot;acc:o43763]	252.492	237.28	1.06411	
585	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [source:swissprot;acc:p31314]	252.492	237.28	1.06411	
586	hect domain containing protein 1 (fragment). [source:swissprot;acc:q9ult8]	252.492	237.28	1.06411	
587	homeobox protein barh-like 2. [source:swissprot;acc:q9umq3]	252.492	237.28	1.06411	
588	shwachman-bodian-diamond syndrome protein (cgi-97). [source:swissprot;acc:q9y3a5]	230.362	216.557	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]	214.546	228.215	1.06371	
590	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	204.279	217.215	1.06333	
591	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [source:swissprot;acc:p78346]	230.439	216.72	1.0633	
592	protein phosphatase 1, regulatory subunit 7; sds22. [source:refseq;acc:nm_002712]	97.4011	91.63	1.06298	
593	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [source:swissprot;acc:q01658]	218.406	232.118	1.06278	
594	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [source:swissprot;acc:o60508]	210.136	223.282	1.06256	
595	vav proto-oncogene. [source:swissprot;acc:p15498]	199.849	212.2	1.0618	
596	vav-3 protein. [source:swissprot;acc:q9ukw4]	199.908	212.253	1.06175	
597	vav-2 protein. [source:swissprot;acc:p52735]	200.212	212.526	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]	234.095	248.463	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]	234.095	248.463	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]	234.095	248.463	1.06138	
601	vam6/vps39-like protein (hvam6p). [source:swissprot;acc:q96jc1]	218.792	206.274	1.06069	
602	microtubule-associated protein 4 (map 4). [source:swissprot;acc:p27816]	218.792	206.274	1.06069	
603	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [source:swissprot;acc:q9uju2]	212.945	225.829	1.0605	
604	60s ribosomal protein l15. [source:swissprot;acc:p39030]	230.978	217.862	1.0602	
605	histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	233.441	247.47	1.0601	
606	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	233.441	247.47	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]	233.441	247.47	1.0601	
608	histone h2b. [source:refseq;acc:nm_175055]	233.441	247.47	1.0601	
609	histone h2b.s (h2b/s). [source:swissprot;acc:p57053]	233.441	247.47	1.0601	
610	histone h2b.d (h2b/d). [source:swissprot;acc:q99877]	233.441	247.47	1.0601	
611	histone h3.4 (h3t) (h3/t) (h3/g). [source:swissprot;acc:q16695]	233.441	247.47	1.0601	
612	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [source:refseq;acc:nm_170610]	233.441	247.47	1.0601	

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/