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 2480 to 2529 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
2480	ARHGAP1	rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960]	218.093	218.72	1.00287
2481	KLC2	kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6]
2482	KIF5B	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176]
2483	KIF5C	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282]
2484	KIF5A	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840]
2485	KLC1	kinesin light chain 1 (klc 1). [swissprot;acc:q07866]
2486	GTF3A	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]
2487	EXOC1	exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]
2488	no value	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	194.527	195.08	1.00284
2489		dc11 protein. [refseq;acc:nm_020186]
2490	APPBP1	amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905]
2491	ALAS2	5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557]
2492	UBE1C	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968]
2493	UBE1	ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314]
2494	SLC25A12	calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746]
2495	HHAT	melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]
2496	ALAS1	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]
2497	SLC25A13	calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0]
2498	NDUFAB1	acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561]
2499	NOB1	nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062]	231.414	230.76	1.00283
2500	BIRC5	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	218.949	219.552	1.00275
2501	ZMYND8	protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [swissprot;acc:q9ulu4]	217.398	216.809	1.00272
2502	ZMYND11	adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326]	217.417	216.844	1.00264
2503	PSMC1	26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527]	215.581	216.137	1.00258
2504	TNS1	tensin. [refseq;acc:nm_022648]	218.238	217.682	1.00255
2505	CBX5	chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973]	187.853	188.326	1.00252
2506	C10orf83	44050 protein. [refseq;acc:nm_178832]	151.386	151.009	1.0025
2507	PPP1R8	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]
2508	CEECAM1	cerebral cell adhesion molecule. [refseq;acc:nm_016174]	194.349	193.871	1.00247
2509	CBX3	chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185]	187.902	188.366
2510	GRPEL2	grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5]	234.384	234.948	1.00241
2511	GRPEL1	grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7]
2512	SMARCD2	swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077]
2513	SMARCD3	swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]
2514	SMARCD1	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]
2515	DFFB	dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075]	215.835	216.341	1.00234
2516	ADAMTS9	adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4]
2517	DFFA	dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273]
2518	ANK3	ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955]
2519	ANK2	ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484]
2520	ARL3	adp-ribosylation factor-like protein 3. [swissprot;acc:p36405]
2521	no value	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	201.96	201.488
2522	UNC119	unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432]	215.835	216.341
2523	KPNB1	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]	201.96	201.488
2524	TBL1X	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]
2525	PSMD8	26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]	215.835	216.341
2526	TBL1Y	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	201.96	201.488
2527	TKTL1	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854]	209.143	208.659	1.00232
2528	SCRIB	scribble. [refseq;acc:nm_015356]	221.782	222.291	1.0023
2529	LRRC1	lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214]	221.776	222.283	1.00229

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.