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 425 to 474 of 502 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 0

Rank	Hugo	description	red	green	network_comparison
425	SCRIB	scribble. [refseq;acc:nm_015356]	12370.5	12719	1.02817
426	no value	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	9412.67	9676.67	1.02805
427		apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	11276.1	11582.7	1.02719
428	CSTF2	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	11982.7	12301.2	1.02658
429	no value	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	12318.7	12631.5	1.02539
430		splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	11621.7	11913.4	1.0251
431		histone deacetylase 2 (hd2). [swissprot;acc:q92769]	10043.7	9799.17	1.02495
432	FBN3	fibrillin 3. [refseq;acc:nm_032447]	930	953	1.02473
433	no value	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	772	754	1.02387
434		elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	10028.5	10261.5	1.02323
435	HIST2H2BA	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	8770.94	8574.04	1.02296
436	no value	histone h2b.d (h2b/d). [swissprot;acc:q99877]	8770.82	8574.19	1.02293
437		histone h2b.s (h2b/s). [swissprot;acc:p57053]	8770.41	8574.66	1.02283
438		histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	7759.36	7586.42	1.0228
439		histone h2b. [refseq;acc:nm_175055]	8770.3	8574.79
440		histone h2b.e (h2b/e). [swissprot;acc:q99879]	8770.28	8574.81
441	HIST1H2BL	histone h2b.c (h2b/c). [swissprot;acc:q99880]	8770.14	8574.98	1.02276
442	no value	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	14570.4	14247.3	1.02268
443		protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	9141.6	8940.14	1.02253
444		formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	14556.7	14237.8	1.0224
445		histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	7965.06	7790.78	1.02237
446		dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
447	CHMP4A	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	12532.2	12808.8	1.02207
448	C19orf56	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]	2939	2876	1.02191
449	ARPC1B	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	9897.12	9690.83	1.02129
450	no value	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	11290.8	11525.8	1.02081
451	CHL1	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	14010.2	13737.2	1.01987
452	no value	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]
453	TAF9	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]
454	LATS1	lats homolog 1. [refseq;acc:nm_004690]	13933.5	14204.8	1.01947
455	no value	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
456		williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	16416.1	16721.6	1.01861
457	NSUN5	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]
458	NSUN5B	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]
459	TSNAX	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]	20875	20495	1.01854
460	no value	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]	20914	20558	1.01732
461		scratch; scratch 1. [refseq;acc:nm_031309]	12164.9	12358.1	1.01588
462		dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	12189.6	12378.3	1.01548
463		dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	5558.06	5473.99	1.01536
464		ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	10076.4	9928.08	1.01494
465		transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	9482.68	9620.66	1.01455
466		aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	1543	1521	1.01446
467		histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	21205	20914	1.01391
468	HIST3H2A	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
469	HIST1H2AA	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
470	H2AFJ	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
471	LGALS4	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	11319.2	11463	1.0127
472	ACOT1	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]	7080.27	7165.6	1.01205
473	GPS1	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]	816	825	1.01103
474	LMBR1L	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	11290.1	11167.6	1.01097

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.