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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 858 to 907 of 3228 in total

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

Rank	description	red	green	network_comparison	
858	syntaxin 12. [source:refseq;acc:nm_177424]	217.446	208.997	1.04043	
859	60s ribosomal protein l39. [source:swissprot;acc:p02404]	234.025	224.958	1.04031	
860	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	234.025	224.958	1.04031	
861	40s ribosomal protein s19. [source:swissprot;acc:p39019]	234.025	224.958	1.04031	
862	60s ribosomal protein l31. [source:swissprot;acc:p12947]	234.025	224.958	1.04031	
863	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19138]	240.194	230.957	1.03999	
864	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19784]	240.194	230.957	1.03999	
865	transcription factor btf3 (rna polymerase b transcription factor 3). [source:swissprot;acc:p20290]	211.961	203.814	1.03997	
866	signal recognition particle 68 kda protein (srp68). [source:swissprot;acc:q9uhb9]	221.306	212.806	1.03994	
867	40s ribosomal protein s3a. [source:swissprot;acc:p49241]	225.689	234.674	1.03981	
868	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [source:swissprot;acc:p53602]	233.298	242.571	1.03975	
869	exocyst complex component sec8. [source:swissprot;acc:q96a65]	217.762	209.449	1.03969	
870	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	211.908	203.832	1.03962	
871	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	110.2	114.552	1.03949	
872	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [source:swissprot;acc:q07244]	224.413	233.272	1.03948	
873	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [source:swissprot;acc:o43172]	224.413	233.272	1.03948	
874	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [source:swissprot;acc:p54619]	212.002	203.954	1.03946	
875	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [source:swissprot;acc:p54646]	212.002	203.954	1.03946	
876	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [source:swissprot;acc:q13131]	212.002	203.954	1.03946	
877	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [source:swissprot;acc:o43741]	212.002	203.954	1.03946	
878	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	212.002	203.954	1.03946	
879	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [source:swissprot;acc:q9y478]	212.002	203.954	1.03946	
880	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	212.002	203.954	1.03946	
881	l-myc-1 proto-oncogene protein. [source:swissprot;acc:p12524]	227.604	219.001	1.03928	
882	n-myc proto-oncogene protein. [source:swissprot;acc:p04198]	227.601	219.008	1.03924	
883	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [source:swissprot;acc:q06546]	227.596	219.017	1.03917	
884	ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [source:swissprot;acc:q06545]	227.596	219.017	1.03917	
885	nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [source:swissprot;acc:o00217]	227.596	219.017	1.03917	
886	elongation of very long chain fatty acids protein 1 (cgi-88). [source:swissprot;acc:q9bw60]	227.596	219.018	1.03917	
887	transducin beta-like 3; wd-repeat protein sazd. [source:refseq;acc:nm_006453]	244.155	234.96	1.03913	
888	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	212.027	204.05	1.03909	
889	alpha-nac protein. [source:sptrembl;acc:q9h009]	212.028	204.053	1.03908	
890	syntaxin 7. [source:swissprot;acc:o15400]	217.181	209.012	1.03908	
891	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	212.028	204.055	1.03907	
892	di-ras2. [source:refseq;acc:nm_017594]	212.028	204.055	1.03907	
893	myc proto-oncogene protein (c-myc). [source:swissprot;acc:p01106]	227.585	219.037	1.03903	
894	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [source:swissprot;acc:q9y285]	217.491	209.323	1.03902	
895	phenylalanine-trna synthetase. [source:refseq;acc:nm_006567]	217.491	209.323	1.03902	
896	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [source:swissprot;acc:p52435]	230.811	239.785	1.03888	
897	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [source:swissprot;acc:o15530]	272.878	283.472	1.03882	
898	60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	229.171	238.048	1.03874	
899	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [source:refseq;acc:nm_032243]	229.171	238.048	1.03874	
900	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [source:swissprot;acc:p10599]	229.171	238.048	1.03874	
901	structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [source:swissprot;acc:q08945]	237.62	228.762	1.03872	
902	chromatin-specific transcription elongation factor large subunit. [source:refseq;acc:nm_007192]	237.62	228.762	1.03872	
903	eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [source:swissprot;acc:o75821]	246.354	237.223	1.03849	
904	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [source:swissprot;acc:q14152]	246.354	237.223	1.03849	
905	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [source:refseq;acc:nm_032959]	230.768	239.632	1.03841	
906	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [source:refseq;acc:nm_145325]	230.764	239.62	1.03838	
907	junction plakoglobin (desmoplakin iii). [source:swissprot;acc:p14923]	223.906	215.653	1.03827	

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/