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	Hugo	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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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	Hugo	description	red	green	network_comparison
580	ZNRD1	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596]	236.751	252.038	1.06457
581	TLX3	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	237.28	252.492	1.06411
582	BARX1	homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
583	OPN4	opsin 4 (melanopsin). [swissprot;acc:q9uhm6]
584	TLX2	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]
585	TLX1	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]
586	HECTD1	hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
587	BARX2	homeobox protein barh-like 2. [swissprot;acc:q9umq3]
588	SBDS	shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	216.557	230.362	1.06375
589	no value	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	214.546	1.06371
590	RRM1	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	217.215	204.279	1.06333
591	RPP30	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	216.72	230.439	1.0633
592	PPP1R7	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	91.63	97.4011	1.06298
593	DR1	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658]	232.118	218.406	1.06278
594	CDC40	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	223.282	210.136	1.06256
595	VAV1	vav proto-oncogene. [swissprot;acc:p15498]	212.2	199.849	1.0618
596	VAV3	vav-3 protein. [swissprot;acc:q9ukw4]	212.253	199.908	1.06175
597	VAV2	vav-2 protein. [swissprot;acc:p52735]	212.526	200.212	1.0615
598	AKT1	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	248.463	234.095	1.06138
599	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). [swissprot;acc:q9y243]
600	AKT2	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	VPS39	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	206.274	218.792	1.06069
602	MAP4	microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
603	LEF1	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	225.829	212.945	1.0605
604	RPL15	60s ribosomal protein l15. [swissprot;acc:p39030]	217.862	230.978	1.0602
605	HIST1H2BL	histone h2b.c (h2b/c). [swissprot;acc:q99880]	247.47	233.441	1.0601
606	HIST2H2BA	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]
607	no value	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	HIST3H3	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]
612	HIST1H2BA	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]
613	no value	histone h2b.e (h2b/e). [swissprot;acc:q99879]
614	HOXA10	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	214.257	202.125	1.06002
615	HOXB9	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]		202.132	1.05999
616	HOXA9	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]
617	HOXC9	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]		202.135	1.05997
618	GABRG3	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]	214.256	202.139	1.05994
619	FOXG1	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]
620	GABRG1	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]		202.14
621	GABRA2	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]
622	GABRA6	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]
623	GABRG2	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]
624	no value	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]		202.139
625	GABRA4	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]		202.14
626	GABRE	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]
627	JMJD6	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]		202.139
628	GABRA1	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]		202.14
629	GABRA3	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
- 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.