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 Network Comparison Type Value Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 6456 in total
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1590 TYMS thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Divided 225.119 228.769 1.01621
1591 no value dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
PMM2 phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Subtracted 217.268 213.842 3.426
1592 GTF2B transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] 228.611 225.185
SDF2 stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] Divided 225.119 228.769 1.01621
1593 SDF2L1 stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8]
ZNHIT3 thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Subtracted 228.611 225.185 3.426
1594 JPH4 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] Divided 222.133 225.731 1.0162
NHP2L1 nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Subtracted 228.611 225.185 3.426
1595 no value adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] Divided 222.134 225.731 1.01619
NUFIP1 nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Subtracted 228.611 225.185 3.426
1596 AP1G1 adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747] Divided 222.134 225.731 1.01619
PMM1 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Subtracted 217.334 213.914 3.42
1597 AP1S3 adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3] Divided 222.134 225.731 1.01619
FOXA1 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] Subtracted 217.322 213.916 3.406
1598 no value heat shock factor binding protein 1. [swissprot;acc:o75506] 216.62 213.22 3.4
AP1S1 adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382] Divided 222.134 225.731 1.01619
1599 CLK2 protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Subtracted 214.984 211.614 3.37
DTNBP1 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Divided 217.871 214.404 1.01617
1600 AP2B1 adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] 222.103 225.675 1.01608
CLK3 protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Subtracted 214.982 211.622 3.36
1601 PMM2 phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Divided 217.268 213.842 1.01602
SHMT1 serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Subtracted 221.045 217.699 3.346
1602 FOXA2 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] 217.233 213.897 3.336
PMM1 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Divided 217.334 213.914 1.01599
1603 no value heat shock factor binding protein 1. [swissprot;acc:o75506] 216.62 213.22 1.01595
EEA1 early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] Subtracted 228.654 231.933 3.279
1604 BUB3 mitotic checkpoint protein bub3. [swissprot;acc:o43684] 221.934 218.658 3.276
CLK2 protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Divided 214.984 211.614 1.01593
1605 FOXA1 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] 217.322 213.916 1.01592
ZNF207 zinc finger protein 207. [swissprot;acc:o43670] Subtracted 221.934 218.658 3.276
1606 APOA1BP apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Divided 207.916 204.662 1.0159
MORF4L2 transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] Subtracted 228.477 231.747 3.27
1607 no value transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] 228.484 231.74 3.256
CLK3 protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Divided 214.982 211.622 1.01588
1608 GSPT1 g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] Subtracted 218.789 215.533 3.256
TMEM189 ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Divided 208.106 204.867 1.01581
1609 APOA1BP apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Subtracted 207.916 204.662 3.254
UGP2 utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Divided 208.113 204.876 1.0158
1610 RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Subtracted 217.446 214.2 3.246
UBE2V2 ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Divided 208.122 204.886 1.01579
1611 CEP70 p10-binding protein. [refseq;acc:nm_024491] 221.313 217.877 1.01577
TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Subtracted 217.446 214.2 3.246
1612 no value enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Divided 221.426 224.902 1.0157
TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Subtracted 217.446 214.2 3.246
1613 FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]
HTATIP2 hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] Divided 182.378 185.241 1.0157
1614 no value sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Subtracted 217.446 214.2 3.246
FOXA2 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Divided 217.233 213.897 1.0156
1615 POLE2 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] 246.38 242.596

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/