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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Gene	Value Type	Network Comparison Type	Rank	network_comparison	Interaction Map	red	description	green	Filtered

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Showing element 663 to 712 of 3228 in total

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

Rank	network_comparison	red	description	green
663	1.12094	6374.65	tubby protein homolog. [swissprot;acc:p50607]	7145.59
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	1.1202	6933.17	transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290]	7766.54
674	1.12006	5549.2	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	6215.42
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	1.11998	6938.22	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	7770.65
679	1.11992	6503.1	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	7282.94
680	1.11986	6503.03	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520]	7282.5
681	1.11976	7170.83	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	8029.64
682	1.1197	5552.92	syntaxin 12. [refseq;acc:nm_177424]	6217.59
683	1.11969	7139.5	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]	7994.06
684	1.11954	4359.82	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884]	4880.99
685	1.1195	9327.58	metaxin 1. [swissprot;acc:q13505]	10442.2
686	1.11949	6920.69	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	7747.63
687		6920.71	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	7747.65
688		6920.67	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	7747.6
689		6920.69	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]	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	1.11943	7725.1	j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330]	8647.74
694			human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]
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). [swissprot;acc:p15822]
696			human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]
697	1.11941	7105.27	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962]	7953.71
698	1.11939	7101.95	armet protein precursor (arginine-rich protein). [swissprot;acc:p55145]	7949.85
699		7101.94	histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]	7949.84
700	1.11936	7161.14	40s ribosomal protein s28. [swissprot;acc:p25112]	8015.92
701	1.11913	7802.31	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060]	8731.82
702	1.11911	7067.46	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963]	7909.27
703	1.11899	6912.56	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	7735.12
704	1.11898	6912.27	alpha-nac protein. [sptrembl;acc:q9h009]	7734.68
705	1.11897	6912.09	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	7734.41
706		6912.08	di-ras2. [refseq;acc:nm_017594]	7734.39
707	1.11781	5317.78	c18b11 homolog (44.9kd). [refseq;acc:nm_152260]	5944.25
708			z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]
709			pp1201 protein. [refseq;acc:nm_022152]
710			lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]
711			sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]
712			sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956]

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.