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 644 to 693 of 3228 in total

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

Rank	description	red	green	network_comparison
644	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701]	4810.85	5414.22	1.12542
645	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711]	4810.71	5413.89	1.12538
646	fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087]	4019.88	4522.61	1.12506
647	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	5167.88	4594.43	1.12481
648	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	5248.07	5901.72	1.12455
649	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]
650	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530]	8362.81	9402.7	1.12435
651	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	5168.43	4597.44	1.1242
652	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
653	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	5560.06	6248.27	1.12378
654	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	4088.63	4593.43	1.12346
655	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
656	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	6139.04	6893.7	1.12293
657	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	6079.26	6824.47	1.12258
658	apical-like protein (apxl protein). [swissprot;acc:q13796]	6088.77	6834.87	1.12254
659	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	6089.21	6835.34	1.12253
660	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	5575.18	6254.85	1.12191
661	step ii splicing factor slu7. [refseq;acc:nm_006425]
662	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4]	6374.65	7145.59	1.12094
663	tubby protein homolog. [swissprot;acc:p50607]
664	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]
665	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]
666	tbc1 domain family member 5. [swissprot;acc:q92609]
667	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]
668	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]
669	numb-like protein (numb-r). [swissprot;acc:q9y6r0]
670	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]
671	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]
672	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]
673	transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290]	6933.17	7766.54	1.1202
674	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	5549.2	6215.42	1.12006
675	sprouty homolog 3 (spry-3). [swissprot;acc:o43610]
676	sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609]
677	sprouty homolog 2 (spry-2). [swissprot;acc:o43597]
678	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	6938.22	7770.65	1.11998
679	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	6503.1	7282.94	1.11992
680	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520]	6503.03	7282.5	1.11986
681	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	7170.83	8029.64	1.11976
682	syntaxin 12. [refseq;acc:nm_177424]	5552.92	6217.59	1.1197
683	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	7139.5	7994.06	1.11969
684	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884]	4359.82	4880.99	1.11954
685	metaxin 1. [swissprot;acc:q13505]	9327.58	10442.2	1.1195
686	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	6920.69	7747.63	1.11949
687	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	6920.71	7747.65
688	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	6920.67	7747.6
689	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]	6920.69	7747.63
690	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]
691	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]
692	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]
693	j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330]	7725.1	8647.74	1.11943

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.