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 486 to 535 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
243 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] High confidence 4246.95 5208.98 1.22652
244 protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Low confidence 8759.92 9314.48 1.06331
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] High confidence 4250.14 5211.25 1.22614
245 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 4251.65 5212.33 1.22595
tumor protein p73-like; tumor protein 63 kda with strong homology to p53; tumor protein p63. [refseq;acc:nm_003722] Low confidence 8509.99 9047.26 1.06313
246 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] High confidence 4252.66 5213.05 1.22583
tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Low confidence 8509.76 9046.87 1.06312
247 cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] 8509.51 9046.45 1.0631
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] High confidence 6416.68 7865.15 1.22574
248 proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 6417.18 7859.6 1.22477
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Low confidence 7615.71 8095.68 1.06302
249 apg3p; pc3-96 protein. [refseq;acc:nm_022488] 10547.4 9924.56 1.06276
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] High confidence 6417.18 7859.59 1.22477
250 large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] Low confidence 6975.98 7412.76 1.06261
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] High confidence 6417.18 7859.6 1.22477
251 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Low confidence 8527.55 9058.09 1.06221
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] High confidence 6417.18 7859.6 1.22477
252 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Low confidence 8492.92 9018.94 1.06194
crk-like protein. [swissprot;acc:p46109] High confidence 6417.18 7859.6 1.22477
253 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Low confidence 8223.39 8732.25 1.06188
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] High confidence 6417.18 7859.59 1.22477
254 dj842g6.2 (novel protein imilar to sel1l (sel-1 (suppressor of lin-12, c.elegans)-like)) (fragment). [sptrembl;acc:q9ugd3] Low confidence 8219.97 8727.87 1.06179
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] High confidence 6417.18 7859.6 1.22477
255 proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]
sel-1 homolog precursor (suppressor of lin-12-like protein) (sel-1l). [swissprot;acc:q9ubv2] Low confidence 8219.95 8727.84 1.06179
256 fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 8216.87 8723.91 1.06171
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] High confidence 6417.19 7859.51 1.22476
257 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 6417.31 7858.12 1.22452
synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] Low confidence 8082.34 8579.93 1.06157
258 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] 9249.74 9818.95 1.06154
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] High confidence 6417.33 7857.93 1.22449
259 neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 6417.81 7852.52 1.22355
oligophrenin 1. [swissprot;acc:o60890] Low confidence 6428.7 6824.22 1.06152
260 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] 9246.23 9814.59 1.06147
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] High confidence 4244.95 5193.42 1.22343
261 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Low confidence 8837.18 9379.17 1.06133
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] High confidence 4247.36 5192.61 1.22255
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] 24896.4 20431.7 1.21852
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Low confidence 6440.08 6834.37 1.06122
263 oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 7424.14 7877.49 1.06106
trs85 homolog. [swissprot;acc:q9y2l5] High confidence 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
diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] Low confidence 6396.44 6786.96 1.06105
265 synaptojanin 2 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 2) (fragment). [swissprot;acc:o15056] 8081.02 8573.8 1.06098
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] High confidence 24806.9 20369.9 1.21782
266 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Low confidence 8817.03 9353.9 1.06089
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] High confidence 24806.9 20369.9 1.21782
267 choline/ethanolaminephosphotransferase. [refseq;acc:nm_006090] Low confidence 8813.83 9348.71 1.06069
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] High confidence 14021.4 11523 1.21682
268 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 24473.9 20127.8 1.21593

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/