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.

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

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Showing element 580 to 629 of 3228 in total

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

Rank	description	red	network_comparison	green
580	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596]	236.751	1.06457	252.038
581	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	237.28	1.06411	252.492
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]	216.557	1.06375	230.362
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]	228.215	1.06371	214.546
590	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	217.215	1.06333	204.279
591	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	216.72	1.0633	230.439
592	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	91.63	1.06298	97.4011
593	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658]	232.118	1.06278	218.406
594	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	223.282	1.06256	210.136
595	vav proto-oncogene. [swissprot;acc:p15498]	212.2	1.0618	199.849
596	vav-3 protein. [swissprot;acc:q9ukw4]	212.253	1.06175	199.908
597	vav-2 protein. [swissprot;acc:p52735]	212.526	1.0615	200.212
598	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	248.463	1.06138	234.095
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]	206.274	1.06069	218.792
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]	225.829	1.0605	212.945
604	60s ribosomal protein l15. [swissprot;acc:p39030]	217.862	1.0602	230.978
605	histone h2b.c (h2b/c). [swissprot;acc:q99880]	247.47	1.0601	233.441
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]
608	histone h2b. [refseq;acc:nm_175055]
609	histone h2b.s (h2b/s). [swissprot;acc:p57053]
610	histone h2b.d (h2b/d). [swissprot;acc:q99877]
611	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]
612	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]
613	histone h2b.e (h2b/e). [swissprot;acc:q99879]
614	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	214.257	1.06002	202.125
615	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]		1.05999	202.132
616	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]
617	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]		1.05997	202.135
618	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]	214.256	1.05994	202.139
619	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]
620	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]			202.14
621	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]
622	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]
623	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]
624	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]			202.139
625	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]			202.14
626	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]
627	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]			202.139
628	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]			202.14
629	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]

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.