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 Gene Value Type description Rank network_comparison green Filtered Interaction Map red
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
network_comparison
green
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 1.00319 205.371 204.717
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 1 0.00001 0.00001
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] 1651 1.01445 215.942 219.062
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 1 0.00001 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 1.00787 214.28 215.967
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 1.02148 213.875 218.47
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 627 1.05994 202.139 214.256
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] 1774 1.01214 225.739 223.032
phosphofurin acidic cluster sorting protein 1 isoform 1; cytosolic sorting protein pacs-1. [refseq;acc:nm_018026] 2805 1 0.00001 0.00001
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] 2362 1.00415 208.037 207.178
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 1.0245 207.637 212.724
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 1.00787 214.28 215.967
phosphoinositide-3-kinase, class 3; vps34; phosphatidylinositol 3-kinase, class 3. [refseq;acc:nm_002647] 3173 1 0.00001 0.00001
phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] 2287 1.00535 205.376 206.475
phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] 2296 1.00521 205.38 206.451
phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] 1915 1.01019 213.571 215.747
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 1913 1.01021 213.564 215.745
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 1.04968 235.583 224.434
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] 1602 1.01599 213.914 217.334
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] 1601 1.01602 213.842 217.268
phosphoribosyl pyrophosphate synthetase-associated protein 1 (prpp synthetase-associated protein 1) (39 kda phosphoribosypyrophosphate synthetase-associated protein) (pap39). [swissprot;acc:q14558] 2869 1 0.00001 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 1.0512 235.027 223.58
phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] 1754 1.01256 217.362 220.091
pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] 1250 1.02437 224.7 219.354
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] 993 1.03362 204.205 211.071
placenta growth factor precursor (plgf). [swissprot;acc:p49763] 3036 1 0.00001 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 1.04578 234.511 224.244
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 1.07057 190.24 177.699
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] 794 1.04578 234.511 224.244
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 1 0.00001 0.00001
pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] 1259 1.02437 224.7 219.354
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 522 1.06891 208.523 222.893
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 2094 1.00765 205.747 207.321
pnas-18. [sptrembl;acc:q9bzu3] 1463 1.01959 164.211 161.056
pogo transposable element with znf domain isoform 1. [refseq;acc:nm_015100] 2932 1 0.00001 0.00001
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 1464 1.01957 213.18 217.351
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 984 1.03379 120.654 116.71
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 994 1.03361 120.772 116.845
polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] 1700 1.01367 214.69 217.624
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 1.02194 223.736 228.644

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/