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 green network_comparison red
Results: HTML CSV LaTeX Showing element 501 to 550 of 3730 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
green
network_comparison
red
251 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] 0 1079.38 1.13498 1225.08
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 1 7859.6 1.22477 6417.18
252 crk-like protein. [swissprot;acc:p46109]
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] 0 1079.38 1.13498 1225.08
253 espin. [refseq;acc:nm_031475] 1225.07
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 1 7859.59 1.22477 6417.18
254 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 0 1495.66 1.13461 1318.22
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 1 7859.6 1.22477 6417.18
255 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 0 1495.22 1.1346 1317.84
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 1 7859.6 1.22477 6417.18
256 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] 7859.51 1.22476 6417.19
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 0 1079.77 1.13418 1224.65
257 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 1 7858.12 1.22452 6417.31
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] 0 759.896 1.13358 861.401
258 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 1337.54 1.13048 1183.16
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 1 7857.93 1.22449 6417.33
259 60s ribosomal protein l23a. [swissprot;acc:p29316] 0 1463.51 1.1297 1295.49
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 1 7852.52 1.22355 6417.81
260 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 5193.42 1.22343 4244.95
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 0 2202 1.1296 1949.36
261 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 1463.55 1.12945 1295.81
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 1 5192.61 1.22255 4247.36
262 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 0 676.971 1.12926 764.479
cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] 1 20431.7 1.21852 24896.4
263 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] 0 1633 1.1286 1843
trs85 homolog. [swissprot;acc:q9y2l5] 1 20431.7 1.21852 24896.4
264 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 4094.57 1.2181 4987.58
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] 0 2957.12 1.12829 3336.48
265 60s ribosomal protein l9. [swissprot;acc:p32969] 1894.01 1.12375 1685.44
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 1 20369.9 1.21782 24806.9
266 aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] 0 1312.91 1.1235 1475.05
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 1 20369.9 1.21782 24806.9
267 ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 11523 1.21682 14021.4
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] 0 1312.91 1.1235 1475.05
268 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 1 20127.8 1.21593 24473.9
far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] 0 538.094 1.12346 604.529
269 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 1367.83 1.12309 1217.92
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 1 5575.52 1.21466 4590.18
270 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 19479.8 1.21358 23640.2
ribosomal protein l10-like protein. [refseq;acc:nm_080746] 0 1367.88 1.12309 1217.96
271 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 1 3093.78 1.21092 2554.89
histone h4. [swissprot;acc:p02304] 0 24446.3 1.12278 21773.1
272 60s ribosomal protein l15. [swissprot;acc:p39030] 753.793 1.12261 846.216
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 1 4669.27 1.21012 3858.52
273 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 3870.8 1.20985 3199.4
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 0 1582.65 1.1218 1410.81
274 brain protein 16. [refseq;acc:nm_016458] 2418.14 1.12172 2155.75
chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 1 2579.49 1.20953 3119.98
275 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]
swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] 0 804.725 1.12172 717.401

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/