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 Rank green Interaction Map description network_comparison red Filtered
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 77072 in total
Network Comparison Type  : Divided
Value Type  : Measured
Rank
green
Interaction Map
description
network_comparison
red
Filtered
251 1079.38 High confidence keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] 1.13498 1225.08 0
1969.49 Low confidence zinc finger protein 74 (hznf7). [swissprot;acc:q16587] 1.19447 2352.49
7859.6 High confidence tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 1.22477 6417.18 1
9058.09 Low confidence kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 1.06221 8527.55
252 1079.38 High confidence star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] 1.13498 1225.08 0
1969.39 Low confidence zinc finger protein 285. [refseq;acc:nm_152354] 1.19447 2352.38
7859.6 High confidence crk-like protein. [swissprot;acc:p46109] 1.22477 6417.18 1
9018.94 Low confidence 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] 1.06194 8492.92
253 1079.38 High confidence espin. [refseq;acc:nm_031475] 1.13498 1225.07 0
1969.43 Low confidence zinc finger protein 117 (zinc finger protein hpf9) (fragment). [swissprot;acc:q03924] 1.19447 2352.42
7859.59 High confidence proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 1.22477 6417.18 1
8732.25 Low confidence fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 1.06188 8223.39
254 1495.66 High confidence 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 1.13461 1318.22 0
1969.43 Low confidence zinc finger protein 141. [swissprot;acc:q15928] 1.19447 2352.42
7859.6 High confidence proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 1.22477 6417.18 1
8727.87 Low confidence dj842g6.2 (novel protein imilar to sel1l (sel-1 (suppressor of lin-12, c.elegans)-like)) (fragment). [sptrembl;acc:q9ugd3] 1.06179 8219.97
255 1495.22 High confidence 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 1.1346 1317.84 0
1969.57 Low confidence zinc finger protein 197 (znf20). [swissprot;acc:o14709] 1.19446 2352.58
7859.6 High confidence proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 1.22477 6417.18 1
8727.84 Low confidence sel-1 homolog precursor (suppressor of lin-12-like protein) (sel-1l). [swissprot;acc:q9ubv2] 1.06179 8219.95
256 1079.77 High confidence keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 1.13418 1224.65 0
1969.57 Low confidence similar to zinc finger protein 85 (zinc finger protein hpf4) (htf1). [refseq;acc:nm_033196] 1.19446 2352.58
7859.51 High confidence 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] 1.22476 6417.19 1
8723.91 Low confidence fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 1.06171 8216.87
257 759.896 High confidence creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] 1.13358 861.401 0
1969.72 Low confidence zinc finger protein mgc21738. [refseq;acc:nm_145044] 1.19445 2352.73
7858.12 High confidence ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 1.22452 6417.31 1
8579.93 Low confidence synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] 1.06157 8082.34
258 1337.54 High confidence 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 1.13048 1183.16 0
1969.86 Low confidence zinc finger protein 257 (bone marrow zinc finger 4) (bmzf-4). [swissprot;acc:q9y2q1] 1.19445 2352.89
7857.93 High confidence homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 1.22449 6417.33 1
9818.95 Low confidence aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] 1.06154 9249.74
259 1463.51 High confidence 60s ribosomal protein l23a. [swissprot;acc:p29316] 1.1297 1295.49 0
1969.86 Low confidence krueppel-related zinc finger protein 1 (hkr1 protein). [swissprot;acc:p10072] 1.19445 2352.89
6824.22 oligophrenin 1. [swissprot;acc:o60890] 1.06152 6428.7 1
7852.52 High confidence neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 1.22355 6417.81
260 1969.68 Low confidence zinc finger protein 354c; krab-zinc finger protein synten. [refseq;acc:nm_014594] 1.19445 2352.69 0
2202 High confidence voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 1.1296 1949.36
5193.42 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 1.22343 4244.95 1
9814.59 Low confidence aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] 1.06147 9246.23
261 1463.55 High confidence c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 1.12945 1295.81 0
1969.64 Low confidence zinc finger protein zfd25. [swissprot;acc:q9uii5] 1.19445 2352.64
5192.61 High confidence signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 1.22255 4247.36 1
9379.17 Low confidence adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 1.06133 8837.18
262 676.971 High confidence adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 1.12926 764.479 0
1969.64 Low confidence zinc finger protein 44 (zinc finger protein kox7) (gonadotropin inducible transcription repressor-2) (giot-2). [swissprot;acc:p15621] 1.19445 2352.64
6834.37 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] 1.06122 6440.08 1
20431.7 High confidence 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] 1.21852 24896.4
263 1633 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] 1.1286 1843 0
1969.78 Low confidence zinc finger protein 62; likely ortholog of mouse zinc finger protein 62. [refseq;acc:nm_152283] 1.19445 2352.8

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/