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 network_comparison green
Results: HTML CSV LaTeX Showing element 2051 to 2100 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
network_comparison
green
1026 limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Subtracted 5396.36 533.05 5929.41
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Divided 5509.89 1.09427 6029.29
1027 opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Subtracted 5406.5 532.92 5939.42
s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] Divided 6123.15 1.09422 6700.05
1028 neurotrimin precursor (hnt). [swissprot;acc:q9p121] Subtracted 5413.63 532.83 5946.46
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Divided 5704 1.09421 6241.36
1029 beta-catenin (pro2286). [swissprot;acc:p35222] 5635.26 1.0942 6166.09
polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Subtracted 4726.38 532.57 5258.95
1030 casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] Divided 5048.33 1.09419 5523.85
electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Subtracted 7919.76 532.25 8452.01
1031 membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] Divided 6136.99 1.09418 6714.98
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Subtracted 6437.99 531.68 6969.67
1032 heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652]
ran binding protein 11. [refseq;acc:nm_016338] Divided 6138.91 1.09418 6717.05
1033 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 6080.91 1.09417 6653.52
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Subtracted 6437.99 531.68 6969.67
1034 heat shock cognate 71 kda protein. [swissprot;acc:p11142]
s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] Divided 6152.88 1.09414 6732.12
1035 beta-catenin (pro2286). [swissprot;acc:p35222] Subtracted 5635.26 530.83 6166.09
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] Divided 5054.73 1.09407 5530.23
1036 fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 6077.65 1.09404 6649.22
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Subtracted 5910.54 530.04 6440.58
1037 monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] Divided 6544.26 1.094 7159.43
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Subtracted 5910.54 530.04 6440.58
1038 myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Divided 5417.95 1.09348 5924.41
phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [swissprot;acc:p15259] Subtracted 5910.54 530.04 6440.58
1039 myb-related protein b (b-myb). [swissprot;acc:p10244] Divided 5418.92 1.09304 5923.09
tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] Subtracted 5719.01 529.59 6248.6
1040 putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305]
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Divided 5421.93 1.09298 5926.08
1041 dead-box protein. [refseq;acc:nm_018665] Subtracted 5719.01 529.59 6248.6
myb-related protein a (a-myb). [swissprot;acc:p10243] Divided 5419.18 1.09294 5922.84
1042 histone h2b.c (h2b/c). [swissprot;acc:q99880] Subtracted 3946.32 529.15 4475.47
similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Divided 5887.52 1.09287 6434.32
1043 15 kda selenoprotein precursor. [swissprot;acc:o60613] 6344.41 1.09283 6933.36
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Subtracted 3946.32 529.15 4475.47
1044 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]
mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] Divided 4757.46 1.09279 5198.91
1045 histone h2b. [refseq;acc:nm_175055] Subtracted 3946.32 529.15 4475.47
immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] Divided 5364.32 1.09279 5862.09
1046 histone h2b.s (h2b/s). [swissprot;acc:p57053] Subtracted 3946.32 529.15 4475.47
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Divided 4757.46 1.09279 5198.91
1047 histone h2b.d (h2b/d). [swissprot;acc:q99877] Subtracted 3946.32 529.15 4475.47
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Divided 4757.46 1.09279 5198.91
1048 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Subtracted 3946.32 529.15 4475.47
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Divided 4757.46 1.09279 5198.91
1049 sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Subtracted 3946.32 529.15 4475.47
1050 histone h2b.e (h2b/e). [swissprot;acc:q99879]
neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Divided 4757.46 1.09279 5198.91

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/