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 493 to 542 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
247 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Subtracted 13241.4 11864 1377.4
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Divided 6416.68 7865.15 1.22574
248 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Subtracted 13241.4 11864 1377.4
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Divided 6417.18 7859.6 1.22477
249 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Subtracted 4405.4 5782.08 1376.68
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Divided 6417.18 7859.59 1.22477
250 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 7859.6
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Subtracted 4578.09 5939.91 1361.82
251 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 4579.34 5940.64 1361.3
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Divided 6417.18 7859.6 1.22477
252 crk-like protein. [swissprot;acc:p46109]
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Subtracted 9648.27 10994.9 1346.63
253 endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 9642.22 10986.4 1344.18
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Divided 6417.18 7859.59 1.22477
254 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Subtracted 9634.98 10976.2 1341.22
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Divided 6417.18 7859.6 1.22477
255 mad protein (max dimerizer). [swissprot;acc:q05195] Subtracted 4455.95 5774.03 1318.08
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Divided 6417.18 7859.6 1.22477
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] 6417.19 7859.51 1.22476
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Subtracted 4456.67 5773.77 1317.1
257 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Divided 6417.31 7858.12 1.22452
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Subtracted 4456.93 5773.67 1316.74
258 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Divided 6417.33 7857.93 1.22449
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Subtracted 4457.06 5773.63 1316.57
259 neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Divided 6417.81 7852.52 1.22355
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Subtracted 4569.48 5885.79 1316.31
260 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 12515.4 11221.1 1294.3
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 4244.95 5193.42 1.22343
261 4247.36 5192.61 1.22255
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Subtracted 4571.89 5864.86 1292.97
262 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] Divided 24896.4 20431.7 1.21852
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Subtracted 4571.89 5864.86 1292.97
263 dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]
trs85 homolog. [swissprot;acc:q9y2l5] Divided 24896.4 20431.7 1.21852
264 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 4987.58 4094.57 1.2181
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Subtracted 12503.3 11212 1291.3
265 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 4638.1 5923.4 1285.3
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Divided 24806.9 20369.9 1.21782
266 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Subtracted 11222.2 9948.93 1273.27
267 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Divided 14021.4 11523 1.21682
268 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Subtracted 11222.2 9948.93 1273.27
cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Divided 24473.9 20127.8 1.21593
269 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Subtracted 4808.79 6074.21 1265.42
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Divided 4590.18 5575.52 1.21466
270 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 23640.2 19479.8 1.21358
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Subtracted 4810.22 6075.04 1264.82
271 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Divided 2554.89 3093.78 1.21092
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Subtracted 4812.01 6076.09 1264.08

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/