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

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

Results: HTML CSV LaTeX

Showing element 633 to 682 of 3228 in total

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

Rank	description	red	green	network_comparison	
633	ferritin light chain (ferritin l subunit). [source:swissprot;acc:p02792]	6228.39	7013.19	1.126	
634	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [source:swissprot;acc:q9y2h0]	6228.39	7013.19	1.126	
635	ferritin heavy polypeptide-like 17. [source:swissprot;acc:q9bxu8]	6228.97	7013.53	1.12595	
636	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]	5713.41	6432.92	1.12593	
637	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	7756.51	8731.76	1.12573	
638	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [source:swissprot;acc:p15531]	7755.69	8730.74	1.12572	
639	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [source:swissprot;acc:p22392]	7753.59	8728.13	1.12569	
640	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	4811.02	5414.64	1.12547	
641	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	4810.85	5414.21	1.12542	
642	atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2]	4810.85	5414.23	1.12542	
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]	4810.85	5414.23	1.12542	
644	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [source: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). [source:swissprot;acc:p30711]	4810.71	5413.89	1.12538	
646	fibrillarin (34 kda nucleolar scleroderma antigen). [source:swissprot;acc:p22087]	4019.88	4522.61	1.12506	
647	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	5167.88	4594.43	1.12481	
648	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [source:swissprot;acc:q12874]	5248.07	5901.72	1.12455	
649	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [source:swissprot;acc:q15459]	5248.07	5901.72	1.12455	
650	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [source:refseq;acc:nm_015530]	8362.81	9402.7	1.12435	
651	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	5168.43	4597.44	1.1242	
652	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	5168.43	4597.44	1.1242	
653	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [source:swissprot;acc:p56192]	5560.06	6248.27	1.12378	
654	histone h3.3 (h3.a) (h3.b) (h3.3q). [source:swissprot;acc:p06351]	4088.63	4593.43	1.12346	
655	dj1099d15.1 (putative dnaj protein). [source:sptrembl;acc:q9h4j9]	4088.63	4593.43	1.12346	
656	apolipoprotein a-i binding protein; apoa-i binding protein. [source: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). [source:swissprot;acc:o14908]	6079.26	6824.47	1.12258	
658	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	6088.77	6834.87	1.12254	
659	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	6089.21	6835.34	1.12253	
660	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [source:swissprot;acc:q15695]	5575.18	6254.85	1.12191	
661	step ii splicing factor slu7. [source:refseq;acc:nm_006425]	5575.18	6254.85	1.12191	
662	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [source:swissprot;acc:q9byg4]	6374.65	7145.59	1.12094	
663	tubby protein homolog. [source:swissprot;acc:p50607]	6374.65	7145.59	1.12094	
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]	6374.65	7145.59	1.12094	
665	numb protein homolog (h-numb) (protein s171). [source:swissprot;acc:p49757]	6374.65	7145.59	1.12094	
666	tbc1 domain family member 5. [source:swissprot;acc:q92609]	6374.65	7145.59	1.12094	
667	tubby related protein 1 (tubby-like protein 1). [source:swissprot;acc:o00294]	6374.65	7145.59	1.12094	
668	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [source:swissprot;acc:q9ubq0]	6374.65	7145.59	1.12094	
669	numb-like protein (numb-r). [source:swissprot;acc:q9y6r0]	6374.65	7145.59	1.12094	
670	tubby related protein 3 (tubby-like protein 3). [source:swissprot;acc:o75386]	6374.65	7145.59	1.12094	
671	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [source:swissprot;acc:q96qk1]	6374.65	7145.59	1.12094	
672	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [source:swissprot;acc:q05513]	6374.65	7145.59	1.12094	
673	transcription factor btf3 (rna polymerase b transcription factor 3). [source:swissprot;acc:p20290]	6933.17	7766.54	1.1202	
674	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	5549.2	6215.42	1.12006	
675	sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	5549.2	6215.42	1.12006	
676	sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	5549.2	6215.42	1.12006	
677	sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	5549.2	6215.42	1.12006	
678	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	6938.22	7770.65	1.11998	
679	adenylosuccinate synthase-like 1. [source:refseq;acc:nm_152328]	6503.1	7282.94	1.11992	
680	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [source: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. [source:refseq;acc:nm_016304]	7170.83	8029.64	1.11976	
682	syntaxin 12. [source:refseq;acc:nm_177424]	5552.92	6217.59	1.1197	

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/