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 Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2401 to 2450 of 8289 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
1201 RAD52 dna repair protein rad52 homolog. [swissprot;acc:p43351] Low confidence 203.852 199.266 1.02301
SDHA succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] High confidence 210.986 216.344 1.0254
1202 DPH2 diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384] 227.274 233.041 1.02537
PIGT phosphatidylinositol glycan class t precursor. [refseq;acc:nm_015937] Low confidence 204.636 200.036 1.023
1203 PI15 protease inhibitor 15 preproprotein; 25 kda trypsin inhibitor. [refseq;acc:nm_015886] 203.323 198.756 1.02298
TNFAIP1 tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] High confidence 219.023 213.606 1.02536
1204 KCTD13 polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] 219.022 213.607 1.02535
R3HDML r3h domain (binds single-stranded nucleic acids) containing-like. [refseq;acc:nm_178491] Low confidence 203.323 198.756 1.02298
1205 KIF21A ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] High confidence 224.805 219.251 1.02533
NXF1 nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Low confidence 197.84 193.402 1.02295
1206 no value integral membrane protein cii-3b. [sptrembl;acc:o75609] High confidence 207.646 212.891 1.02526
CD109 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Low confidence 203.629 208.303 1.02295
1207 NXF5 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 197.868 193.428
SDHC succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] High confidence 207.644 212.888 1.02525
1208 no value signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 224.878 219.342 1.02524
NXF3 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Low confidence 197.863 193.425 1.02294
1209 no value guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] 202.873 198.325 1.02293
SDHB succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] High confidence 207.931 213.175 1.02522
1210 KIF2A kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] 224.764 219.241 1.02519
SNAPC3 snrna activating protein complex 50 kda subunit (snapc 50 kda subunit) (proximal sequence element-binding transcription factor beta subunit) (pse-binding factor beta subunit) (ptf beta subunit). [swissprot;acc:q92966] Low confidence 202.718 198.176 1.02292
1211 ARPC5 arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511] 201.559 197.042
C11orf2 chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] High confidence 214.364 219.759 1.02517
1212 KIF13A kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9]
MFAP1 microfibrillar-associated protein 1. [swissprot;acc:p55081] Low confidence 202.718 198.176 1.02292
1213 COG2 conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746] High confidence 214.364 219.759 1.02517
PRODH2 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Low confidence 198.145 193.707 1.02291
1214 no value kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] High confidence 214.364 219.759 1.02517
EVI1 ecotropic virus integration 1 site protein. [swissprot;acc:q03112] Low confidence 203.266 198.72 1.02288
1215 CETN3 centrin 3. [swissprot;acc:o15182] 197.302 192.899 1.02283
DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] High confidence 218.268 212.916 1.02514
1216 TFAP2A transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549] Low confidence 203.197 198.662 1.02283
ZMIZ1 retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] High confidence 218.269 212.918 1.02513
1217 DHPS deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] Low confidence 201.691 197.19 1.02283
QRSL1 glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] High confidence 211.959 217.258 1.025
1218 FAAH fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519]
TFAP2C transcription factor ap-2 gamma (ap2-gamma) (activating enhancer- binding protein 2 gamma) (transcription factor erf-1). [swissprot;acc:q92754] Low confidence 203.197 198.662 1.02283
1219 COTL1 coactosin-like protein. [swissprot;acc:q14019] High confidence 211.959 217.258 1.025
TFAP2B transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481] Low confidence 203.197 198.662 1.02283
1220 no value histone h4. [swissprot;acc:p02304] 202.096 197.587 1.02282
UNG uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] High confidence 211.959 217.258 1.025
1221 PET112L probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]
TPTE putative protein-tyrosine phosphatase tpte (ec 3.1.3.48). [swissprot;acc:p56180] Low confidence 203.336 198.8 1.02282
1222 ATP1A3 sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] 203.529 198.989
TPD52L1 tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] High confidence 206.774 211.936 1.02496
1223 PLEKHF2 phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Low confidence 204.15 199.597 1.02281
TPD52 tumor protein d52 (n8 protein). [swissprot;acc:p55327] High confidence 206.771 211.926 1.02493
1224 FPGS folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 225.906 231.524 1.02487
TPTE2 tpte and pten homologous inositol lipid phosphatase. [refseq;acc:nm_130785] Low confidence 203.335 198.8 1.02281
1225 DHCR7 7-dehydrocholesterol reductase (ec 1.3.1.21) (7-dhc reductase) (sterol delta-7-reductase) (putative sterol reductase sr-2). [swissprot;acc:q9ubm7] 203.51 198.973 1.0228
UBE2E1 ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] High confidence 166.846 170.989 1.02483

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/