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 683 to 732 of 3228 in total

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

Rank	description	red	green	network_comparison	
683	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [source: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). [source:swissprot;acc:p55884]	4359.82	4880.99	1.11954	
685	metaxin 1. [source:swissprot;acc:q13505]	9327.58	10442.2	1.1195	
686	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [source: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). [source:swissprot;acc:p54646]	6920.71	7747.65	1.11949	
688	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [source:swissprot;acc:q13131]	6920.67	7747.6	1.11949	
689	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [source:swissprot;acc:o43741]	6920.69	7747.63	1.11949	
690	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	6920.69	7747.63	1.11949	
691	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [source:swissprot;acc:q9y478]	6920.69	7747.63	1.11949	
692	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	6920.69	7747.63	1.11949	
693	j kappa-recombination signal binding protein (rbp-j kappa). [source:swissprot;acc:q06330]	7725.1	8647.74	1.11943	
694	human immunodeficiency virus type i enhancer binding protein 3. [source:refseq;acc:nm_024503]	7725.1	8647.74	1.11943	
695	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [source:swissprot;acc:p15822]	7725.1	8647.74	1.11943	
696	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [source:swissprot;acc:p31629]	7725.1	8647.74	1.11943	
697	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [source:swissprot;acc:q99962]	7105.27	7953.71	1.11941	
698	armet protein precursor (arginine-rich protein). [source:swissprot;acc:p55145]	7101.95	7949.85	1.11939	
699	histidine decarboxylase (ec 4.1.1.22) (hdc). [source:swissprot;acc:p19113]	7101.94	7949.84	1.11939	
700	40s ribosomal protein s28. [source:swissprot;acc:p25112]	7161.14	8015.92	1.11936	
701	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [source:swissprot;acc:p55060]	7802.31	8731.82	1.11913	
702	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [source:swissprot;acc:q99963]	7067.46	7909.27	1.11911	
703	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	6912.56	7735.12	1.11899	
704	alpha-nac protein. [source:sptrembl;acc:q9h009]	6912.27	7734.68	1.11898	
705	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	6912.09	7734.41	1.11897	
706	di-ras2. [source:refseq;acc:nm_017594]	6912.08	7734.39	1.11897	
707	c18b11 homolog (44.9kd). [source:refseq;acc:nm_152260]	5317.78	5944.25	1.11781	
708	z-protein (protein cgi-119) (s1r protein). [source:swissprot;acc:q9hc24]	5317.78	5944.25	1.11781	
709	pp1201 protein. [source:refseq;acc:nm_022152]	5317.78	5944.25	1.11781	
710	lifeguard; kiaa0950 protein. [source:refseq;acc:nm_012306]	5317.78	5944.25	1.11781	
711	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [source:swissprot;acc:q12772]	5317.78	5944.25	1.11781	
712	sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [source:swissprot;acc:p36956]	5317.78	5944.25	1.11781	
713	upf0202 protein kiaa1709. [source:swissprot;acc:q9h0a0]	3996.81	4465.61	1.11729	
714	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	5222.71	5834.57	1.11715	
715	dendritic cell protein. [source:refseq;acc:nm_006360]	6593.17	7364.55	1.117	
716	potential carboxypeptidase-like protein x2 precursor. [source:swissprot;acc:q8n436]	6593.17	7364.55	1.117	
717	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [source:swissprot;acc:p15169]	6593.17	7364.55	1.117	
718	cpz gene product. [source:refseq;acc:nm_003652]	6593.17	7364.55	1.117	
719	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [source:swissprot;acc:p16870]	6593.17	7364.55	1.117	
720	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [source:swissprot;acc:q96sm3]	6593.17	7364.55	1.117	
721	syntaxin 7. [source:swissprot;acc:o15400]	5580.97	6233.52	1.11692	
722	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [source:swissprot;acc:p49590]	8061.05	9002.33	1.11677	
723	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [source:swissprot;acc:p12081]	8056.09	8996.46	1.11673	
724	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [source:swissprot;acc:q9y285]	5384.41	6012.82	1.11671	
725	phenylalanine-trna synthetase. [source:refseq;acc:nm_006567]	5384.41	6012.82	1.11671	
726	dna mismatch repair protein mlh3 (mutl protein homolog 3). [source:swissprot;acc:q9uhc1]	6327.86	7064.13	1.11635	
727	60s ribosomal protein l24 (l30). [source:swissprot;acc:p38663]	7087.23	7911.25	1.11627	
728	hcv ns3-transactivated protein 1. [source:refseq;acc:nm_019048]	6000.23	6696.89	1.11611	
729	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [source:swissprot;acc:p38606]	6000.23	6696.89	1.11611	
730	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [source:swissprot;acc:p08243]	6000.23	6696.89	1.11611	
731	methyltransferase like 2. [source:refseq;acc:nm_018396]	13241.4	11864	1.1161	
732	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	13241.4	11864	1.1161	

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/