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 description Rank green network_comparison red Filtered Interaction Map
Results: HTML CSV LaTeX Showing element 2001 to 2050 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
green
network_comparison
red
phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] 2449 205.371 1.00319 204.717
phosphatidylethanolamine-binding protein (pebp) (prostatic binding protein) (hcnppp) (neuropolypeptide h3) (raf kinase inhibitor protein) (rkip) [contains: hippocampal cholinergic neurostimulating peptide (hcnp)]. [swissprot;acc:p30086] 3162 0.00001 1 0.00001
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] 1651 215.942 1.01445 219.062
phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] 1656
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] 1653
phosphatidylinositol glycan class t precursor. [refseq;acc:nm_015937] 3024 0.00001 1 0.00001
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 2080 214.28 1.00787 215.967
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] 2079
phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] 1391 213.875 1.02148 218.47
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 627 202.139 1.05994 214.256
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] 1774 225.739 1.01214 223.032
phosphofurin acidic cluster sorting protein 1 isoform 1; cytosolic sorting protein pacs-1. [refseq;acc:nm_018026] 2805 0.00001 1 0.00001
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] 2362 208.037 1.00415 207.178
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] 2359 208.056 207.196
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] 1233 207.637 1.0245 212.724
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] 1234
phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645] 2082 214.28 1.00787 215.967
phosphoinositide-3-kinase, class 3; vps34; phosphatidylinositol 3-kinase, class 3. [refseq;acc:nm_002647] 3173 0.00001 1 0.00001
phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] 2287 205.376 1.00535 206.475
phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] 2296 205.38 1.00521 206.451
phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] 1915 213.571 1.01019 215.747
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 1913 213.564 1.01021 215.745
phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2] 1914
phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] 758 235.583 1.04968 224.434
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] 1602 213.914 1.01599 217.334
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] 1601 213.842 1.01602 217.268
phosphoribosyl pyrophosphate synthetase-associated protein 1 (prpp synthetase-associated protein 1) (39 kda phosphoribosypyrophosphate synthetase-associated protein) (pap39). [swissprot;acc:q14558] 2869 0.00001 1 0.00001
phosphoribosyl pyrophosphate synthetase-associated protein 2 (prpp synthetase-associated protein 2) (41 kda phosphoribosypyrophosphate synthetase-associated protein) (pap41). [swissprot;acc:o60256] 2943
phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] 739 235.027 1.0512 223.58
phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] 1754 217.362 1.01256 220.091
pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] 1250 224.7 1.02437 219.354
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] 993 204.205 1.03362 211.071
placenta growth factor precursor (plgf). [swissprot;acc:p49763] 3036 0.00001 1 0.00001
placental protein 11 precursor (ec 3.4.21.-) (pp11). [swissprot;acc:p21128] 3076
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] 796 234.511 1.04578 224.244
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 510 190.24 1.07057 177.699
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] 794 234.511 1.04578 224.244
platelet-activating factor acetylhydrolase ib alpha subunit (ec 3.1.1.47) (paf acetylhydrolase 45 kda subunit) (paf-ah 45 kda subunit) (paf-ah alpha) (pafah alpha) (lissencephaly-1 protein) (lis- 1). [swissprot;acc:p43034] 3221 0.00001 1 0.00001
pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] 1259 224.7 1.02437 219.354
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 522 208.523 1.06891 222.893
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 2094 205.747 1.00765 207.321
pnas-18. [sptrembl;acc:q9bzu3] 1463 164.211 1.01959 161.056
pogo transposable element with znf domain isoform 1. [refseq;acc:nm_015100] 2932 0.00001 1 0.00001
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 1464 213.18 1.01957 217.351
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 984 120.654 1.03379 116.71
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 994 120.772 1.03361 116.845
polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] 1700 214.69 1.01367 217.624
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 1696
polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310] 1699
polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] 1368 223.736 1.02194 228.644

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/