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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3013 to 3062 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
754 no value myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Measured 4565.34 5085.92 1.11403
BCAT1 branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] Squared 23958.6 27945.1 1.16639
PRKAG3 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Rooted 66.9737 71.4637 1.06704
SPCS2 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] Ranked 224.434 235.583 1.04968
755 BCAT2 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] Squared 23966.4 27952.2 1.16631
NOL6 nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Measured 4079.81 4545.01 1.11402
PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Rooted 66.9737 71.4637 1.06704
UMPS uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] Ranked 224.434 235.583 1.04968
756 CLPTM1 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]
PAPD5 topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Measured 4725.28 5261.06 1.11339
PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Rooted 66.9737 71.4637 1.06704
TLE4 transducin-like enhancer protein 4. [swissprot;acc:q04727] Squared 31298 36502 1.16627
757 BPI bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Ranked 224.434 235.583 1.04968
SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Squared 20248.9 23608.3 1.16591
SRP68 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Measured 5622.89 6260.02 1.11331
UQCRC1 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Rooted 60.4457 64.4918 1.06694
758 KLF5 krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Squared 20248.9 23608.3 1.16591
PLTP phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] Ranked 224.434 235.583 1.04968
POLE2 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] Measured 3760.3 4185.82 1.11316
TRMU trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Rooted 96.6463 103.103 1.06681
759 no value nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 66.9416 71.4055 1.06668
COPA coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Squared 49280.5 42272.7 1.16578
OSTF1 osteoclast stimulating factor 1. [swissprot;acc:q92882] Ranked 231.809 243.289 1.04952
PFKP 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Measured 4254.62 4736.03 1.11315
760 ATP6V0D2 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] 5870.2 6533.39 1.11298
DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Rooted 66.9397 71.4023 1.06667
NAT10 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Ranked 246.055 234.458 1.04946
RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Squared 21186.4 24698.3 1.16576
761 no value alpha-nac protein. [sptrembl;acc:q9h009] Rooted 66.9404 71.4035 1.06667
CBLB signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Ranked 213.325 203.303 1.0493
EIF5B translation initiation factor if-2. [swissprot;acc:o60841] Measured 5811.51 6467.62 1.1129
TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Squared 21186.4 24698.3 1.16576
762 CBL cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Ranked 213.256 203.237 1.0493
DIRAS2 di-ras2. [refseq;acc:nm_017594] Rooted 66.9397 71.4022 1.06666
PMS2 pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Measured 6231.31 6933.9 1.11275
TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Squared 21186.4 24698.3 1.16576
763 DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Rooted 60.3269 64.3387 1.0665
FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Squared 21186.4 24698.3 1.16576
N6AMT1 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Ranked 228.78 218.091 1.04901
PFKM 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] Measured 4250.54 4729.67 1.11272
764 no value sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Squared 21186.4 24698.3 1.16576
CBS cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Rooted 63.5181 67.7402 1.06647
PFKL 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] Measured 4250.18 4729.12 1.11269
PRPF3 u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Ranked 222.082 211.707 1.04901
765 HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 229.045 218.343
POLS polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Measured 4726.38 5258.95 1.11268
RHOC transforming protein rhoc (h9). [swissprot;acc:p08134] Rooted 63.5181 67.7402 1.06647
SREBF1 sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Squared 21186.4 24698.3 1.16576
766 ATP5C1 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 24509.4 28571.6 1.16574
TMEM189 ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Measured 6691.93 7445.09 1.11255

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
- Hugo is the HGNC identifier if it exists
- 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/