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

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Showing element 2558 to 2607 of 3228 in total

Network Comparison Type

: Divided
Value Type

: Ranked
Filtered

: 1
Interaction Map

: High confidence

description	Rank	green	network_comparison	red
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	204	228.752	1.13516	201.515
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	363	211.131	1.09639	231.481
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	588	230.362	1.06375	216.557
signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	2695	215.384	1.00075	215.545
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9]	866	212.806	1.03994	221.306
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	450	218.837	1.07815	235.94
	458	218.925	1.07764	235.922
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	1208	219.342	1.02524	224.878
signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224]	1315	227.752	1.02326	222.574
signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763]	1313	227.75		222.573
signal transducer and activator of transcription 4. [swissprot;acc:q14765]	1314	227.751		222.573
signal transducer and activator of transcription 5a. [swissprot;acc:p42229]	1318	227.673	1.02304	222.546
signal transducer and activator of transcription 5b. [swissprot;acc:p51692]	1320	227.667	1.02302	222.544
signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226]	1316	227.739	1.02323	222.569
signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]	2393	182.962	1.00382	182.266
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843]	2406	183.232	1.00366	182.563
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	761	203.303	1.0493	213.325
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]	2164	214.481	1.00673	215.925
similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]	2628	225.195	1.00135	224.891
similar to cg5057 gene product. [sptrembl;acc:q9btt4]	2984	0.00001	1	0.00001
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	1908	193.394	1.01034	191.415
similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245]	1436	214.493	1.02022	218.829
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]	631	202.141	1.05993	214.256
similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428]	1813	214.35	1.01168	216.854
similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6]	2671	216.067	1.00102	216.288
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5]	2071	215.807	1.0081	217.555
similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2]	1750	213.57	1.01264	216.27
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	3032	0.00001	1	0.00001
similar to mob-lak. [refseq;acc:nm_145279]	2937	0.00001	1	0.00001
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61]	803	221.785	1.04425	212.386
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557]	1957	213.703	1.00978	211.633
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	1090	232.88	1.02945	226.218
similar to trna synthetase class ii. [refseq;acc:nm_152268]	2714	220.348	1.00056	220.224
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	1086	243.679	1.02958	236.679
sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422]	1454	211.089	1.01964	207.024
sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864]	2207	200.413	1.00645	199.129
single-minded homolog 1. [swissprot;acc:p81133]	675	214.355	1.05664	226.497
sipl protein. [refseq;acc:nm_018269]	2247	207.346	1.00609	208.609
sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238]	2731	212.985	1.0003	212.922
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	935	224.372	1.03611	232.473
skd1 protein (vacuolar sorting protein 4b). [swissprot;acc:o75351]	3037	0.00001	1	0.00001
skeletal muscle and kidney enriched inositol phosphatase isoform 1; 43-kda form skeletal muscle and kidney enriched inositol phosphatase. [refseq;acc:nm_016532]	2994	0.00001	1	0.00001
skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643]	1198	276.454	1.02546	269.59
skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192]	1195	276.493	1.02554	269.608
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]	2332	230.294	1.00452	229.258
small edrk-rich factor 2. [refseq;acc:nm_005770]	2947	0.00001	1	0.00001
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	2637	186.84	1.00126	187.075
small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	2748	189.531	1.00017	189.563
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	891	204.055	1.03907	212.028
small nuclear ribonucleoprotein associated protein n (snrnp-n) (sm protein n) (sm-n) (smn) (sm-d) (tissue-specific splicing protein). [swissprot;acc:p14648]	3004	0.00001	1	0.00001

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.

- http://analysis.yellowcouch.org/