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

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Showing element 94 to 143 of 3228 in total

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

Rank	description	red	green	network_comparison
94	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	4247.86	5941.88	1.39879
95	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	2397.19	3343.62	1.39481
96	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	4110.14	5694.99	1.3856
97	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	2820.51	3897.1	1.3817
98	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	2353.63	3225.65	1.3705
99	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]
100	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]
101	cullin homolog 2 (cul-2). [swissprot;acc:q13617]
102	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]
103	cullin homolog 1 (cul-1). [swissprot;acc:q13616]
104	musashi 2 isoform a. [refseq;acc:nm_138962]	4241.57	5810.79	1.36996
105	musashi 1. [refseq;acc:nm_002442]
106	nuclear protein ukp68. [refseq;acc:nm_024824]
107	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	4266.04	5843.51	1.36977
108	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	4366.44	5899.76	1.35116
109	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]
110	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]
111	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]
112	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]
113	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
114	huntingtin interacting protein c. [refseq;acc:nm_012272]	4300.47	5807.72	1.35048
115	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	21185	28492	1.34491
116	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]
117	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]
118	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]
119	mitochondrial solute carrier protein. [refseq;acc:nm_145305]
120	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	5136.78	6895.98	1.34247
121	transcription factor jun-b. [swissprot;acc:p17275]	5579.18	7488.4	1.3422
122	high-mobility group 20a. [refseq;acc:nm_018200]	5140.14	6893.53	1.34112
123	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	24260.3	18172.1	1.33503
124	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	24255.7	18168.9	1.33501
125	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]
126	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	24250	18164.9	1.33499
127	transcription factor jun-d. [swissprot;acc:p17535]	5638.2	7523.39	1.33436
128	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	4355.61	5810.82	1.3341
129	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	4358.13	5811.49	1.33348
130	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	2234.68	2978.53	1.33287
131	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	2234.73	2978.57	1.33285
132	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	2236.61	2980.35	1.33253
133	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	23421.5	17580.4	1.33225
134	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	21785.2	16426.1	1.32626
135	apg3p; pc3-96 protein. [refseq;acc:nm_022488]
136	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	3620.77	4763.34	1.31556
137	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]
138	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	2755.15	2094.3	1.31555
139	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	2759.61	2099.49	1.31442
140	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	2760.28	2100.27	1.31425
141	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	4405.4	5782.08	1.3125
142	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	9276.47	7090.37	1.30832
143	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	9275.1	7089.65	1.30826

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.