MK5 Microarray Data

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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank	Gene	description	Value Type	Network Comparison Type	Interaction Map	Filtered	green	red	network_comparison

Results: HTML CSV LaTeX

Showing element 558 to 607 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	green	red	network_comparison
558	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	144.041	135.087	1.06628
559	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	194.452	207.309	1.06612
560	son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889]	193.021	205.74	1.06589
561	son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]	193.183	205.89	1.06578
562	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	207.121	220.744	1.06577
563	calcyphosine. [swissprot;acc:q13938]
564	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]
565	sedlin. [swissprot;acc:o14582]	121.261	129.219	1.06563
566	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
567	bet3 homolog. [swissprot;acc:o43617]
568	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	212.38	226.3	1.06554
569	t54 protein. [swissprot;acc:q92917]
570	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	215.631	229.709	1.06529
571	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926]	254.099	238.529	1.06528
572	cbf1 interacting corepressor. [refseq;acc:nm_004882]	213.945	227.86	1.06504
573	evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]
574	preimplantation protein 3; likely ortholog of preimplantation protein 3. [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). [swissprot;acc:q9ubs4]
576	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	250.419	235.18	1.0648
577	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [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). [swissprot;acc:q13435]
579	zinc finger protein t86. [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. [refseq;acc:nm_014596]	252.038	236.751	1.06457
581	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	252.492	237.28	1.06411
582	homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
583	opsin 4 (melanopsin). [swissprot;acc:q9uhm6]
584	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]
585	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]
586	hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
587	homeobox protein barh-like 2. [swissprot;acc:q9umq3]
588	shwachman-bodian-diamond syndrome protein (cgi-97). [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). [swissprot;acc:q9y333]	214.546	228.215	1.06371
590	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [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). [swissprot;acc:p78346]	230.439	216.72	1.0633
592	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	97.4011	91.63	1.06298
593	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658]	218.406	232.118	1.06278
594	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	210.136	223.282	1.06256
595	vav proto-oncogene. [swissprot;acc:p15498]	199.849	212.2	1.0618
596	vav-3 protein. [swissprot;acc:q9ukw4]	199.908	212.253	1.06175
597	vav-2 protein. [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). [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). [swissprot;acc:q9y243]
600	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]
601	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	218.792	206.274	1.06069
602	microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
603	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	212.945	225.829	1.0605
604	60s ribosomal protein l15. [swissprot;acc:p39030]	230.978	217.862	1.0602
605	histone h2b.c (h2b/c). [swissprot;acc:q99880]	233.441	247.47	1.0601
606	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]
607	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.