Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1283 to 1332 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
642	atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2]	Divided	4810.85	5414.23	1.12542	
642	elongation of very long chain fatty acids protein 1 (cgi-88). [source:swissprot;acc:q9bw60]	Subtracted	4890.55	5610.96	720.41	
643	polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [source:refseq;acc:nm_019025]	Divided	4810.85	5414.23	1.12542	
643	scratch; scratch 1. [source:refseq;acc:nm_031309]	Subtracted	7281.6	8001.64	720.04	
644	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [source:swissprot;acc:p53701]	Divided	4810.85	5414.22	1.12542	
644	proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [source:swissprot;acc:p28066]	Subtracted	5713.41	6432.92	719.51	
645	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [source:swissprot;acc:p30711]	Divided	4810.71	5413.89	1.12538	
645	myc proto-oncogene protein (c-myc). [source:swissprot;acc:p01106]	Subtracted	4892.16	5611.48	719.32	
646	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [source:sptrembl;acc:q9nq03]	Subtracted	7273.78	7991.72	717.94	
646	fibrillarin (34 kda nucleolar scleroderma antigen). [source:swissprot;acc:p22087]	Divided	4019.88	4522.61	1.12506	
647	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	Subtracted	2411.93	1695.45	716.48	
647	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	Divided	5167.88	4594.43	1.12481	
648	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [source:swissprot;acc:p32929]	Subtracted	2414.22	1698.12	716.1	
648	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [source:swissprot;acc:q12874]	Divided	5248.07	5901.72	1.12455	
649	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [source:refseq;acc:nm_004980]	Subtracted	2414.77	1698.75	716.02	
649	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [source:swissprot;acc:q15459]	Divided	5248.07	5901.72	1.12455	
650	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [source:refseq;acc:nm_015530]	Divided	8362.81	9402.7	1.12435	
650	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [source:refseq;acc:nm_004979]	Subtracted	2416.53	1700.8	715.73	
651	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	Divided	5168.43	4597.44	1.1242	
651	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [source:swissprot;acc:p41227]	Subtracted	4509.54	5223.95	714.41	
652	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	Subtracted	6456.35	7169.75	713.4	
652	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	Divided	5168.43	4597.44	1.1242	
653	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [source:swissprot;acc:p11388]	Subtracted	6441.17	7154.55	713.38	
653	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [source:swissprot;acc:p56192]	Divided	5560.06	6248.27	1.12378	
654	histone h3.3 (h3.a) (h3.b) (h3.3q). [source:swissprot;acc:p06351]	Divided	4088.63	4593.43	1.12346	
654	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	Subtracted	6455.66	7168.82	713.16	
655	dj1099d15.1 (putative dnaj protein). [source:sptrembl;acc:q9h4j9]	Divided	4088.63	4593.43	1.12346	
655	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [source:swissprot;acc:q02880]	Subtracted	6441.14	7154.13	712.99	
656	apolipoprotein a-i binding protein; apoa-i binding protein. [source:refseq;acc:nm_144772]	Divided	6139.04	6893.7	1.12293	
656	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	Subtracted	6455.02	7167.96	712.94	
657	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [source:refseq;acc:nm_013366]	Subtracted	10341.2	9630.35	710.85	
657	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	Divided	6079.26	6824.47	1.12258	
658	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	Divided	6088.77	6834.87	1.12254	
658	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [source:swissprot;acc:o95817]	Subtracted	4522.71	5233.14	710.43	
659	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	Subtracted	4858.96	5568.85	709.89	
659	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	Divided	6089.21	6835.34	1.12253	
660	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	Subtracted	4864.25	5573.62	709.37	
660	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [source:swissprot;acc:q15695]	Divided	5575.18	6254.85	1.12191	
661	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [source:swissprot;acc:q09028]	Subtracted	4869.15	5578.02	708.87	
661	step ii splicing factor slu7. [source:refseq;acc:nm_006425]	Divided	5575.18	6254.85	1.12191	
662	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [source:swissprot;acc:o43639]	Subtracted	6776.85	7485.55	708.7	
662	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [source:swissprot;acc:q9byg4]	Divided	6374.65	7145.59	1.12094	
663	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [source:swissprot;acc:p48735]	Subtracted	7937.72	8646.38	708.66	
663	tubby protein homolog. [source:swissprot;acc:p50607]	Divided	6374.65	7145.59	1.12094	
664	pms1 protein homolog 2 (dna mismatch repair protein pms2). [source:swissprot;acc:p54278]	Subtracted	6231.31	6933.9	702.59	
664	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [source:swissprot;acc:p41743]	Divided	6374.65	7145.59	1.12094	
665	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	Subtracted	4108.15	4808.93	700.78	
665	numb protein homolog (h-numb) (protein s171). [source:swissprot;acc:p49757]	Divided	6374.65	7145.59	1.12094	
666	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [source:swissprot;acc:q15668]	Subtracted	6781.05	7480.15	699.1	
666	tbc1 domain family member 5. [source:swissprot;acc:q92609]	Divided	6374.65	7145.59	1.12094	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/