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 3808 to 3857 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
952 TOM1L2 target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] Ranked 217.252 209.83 1.03537
953 CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Rooted 93.6481 88.4638 1.0586
CSNK1A1L casein kinase i alpha s-like. [refseq;acc:nm_145203] Measured 4906.33 5382.5 1.09705
EIF3G eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Squared 16131.6 18602.2 1.15315
EXOSC10 polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] Ranked 198.494 205.466 1.03512
954 CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Rooted 93.6382 88.4565 1.05858
CSNK1A1 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Measured 4906.33 5382.5 1.09705
EIF3A eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Squared 16131.6 18602.2 1.15315
GSTZ1 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Ranked 267.447 276.773 1.03487
955 no value dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] Squared 24856.2 28661.3 1.15308
uridine kinase-like 1. [swissprot;acc:q9nwz5] Measured 5548.78 6086.89 1.09698
CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Rooted 93.5947 88.4244 1.05847
MRPL27 mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] Ranked 231.163 239.205 1.03479
956 CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Rooted 93.5901 88.4209 1.05846
FMO3 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Measured 5364.77 5884.89 1.09695
SORBS3 vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Ranked 211.812 204.732 1.03458
SPTLC2 serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] Squared 24804.6 28595.4 1.15283
957 ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Ranked 129.913 134.399 1.03453
CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Rooted 93.5619 88.4001 1.05839
NARS asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] Squared 26822.8 30911.4 1.15243
SSRP1 structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] Measured 4483.26 4917.77 1.09692
958 ESRRA steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Rooted 82.1645 86.9566 1.05832
RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Ranked 129.921 134.406 1.03452
SEPHS2 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Squared 29830.2 34375.9 1.15239
SUPT16H chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Measured 4483.26 4917.77 1.09692
959 no value guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] Ranked 237.558 229.677 1.03431
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Measured 4379.28 4803.59 1.09689
MICAL2 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Squared 29830.2 34375.9 1.15239
WBP2 ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Rooted 62.1275 65.7481 1.05828
960 INPP4B inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Squared 29830.2 34375.9 1.15239
NDUFB9 nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Rooted 66.4035 70.2633 1.05813
PRKCE protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Measured 11773 10733.2 1.09688
ZRF1 zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Ranked 237.558 229.677 1.03431
961 PPIB peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Measured 11773 10733.2 1.09688
PPP2R5E serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Ranked 130.066 134.527 1.0343
RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Rooted 98.7609 93.3602 1.05785
SEPHS1 selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Squared 29830.2 34375.9 1.15239
962 CCNG2 cyclin g2. [swissprot;acc:q16589] Ranked 130.066 134.527 1.0343
INPP4A inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Squared 29830.2 34375.9 1.15239
OGT udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Measured 11773 10733.2 1.09688
PFDN5 prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Rooted 57.5529 60.879 1.05779
963 no value prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
CCNG1 cyclin g1 (cyclin g). [swissprot;acc:p51959] Ranked 130.066 134.527 1.0343
COX4I1 cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] Measured 11773 10733.2 1.09688
TKT transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] Squared 23594.2 27188.9 1.15236
964 COX4I2 cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Measured 11773 10733.2 1.09688
IPMK inositol polyphosphate multikinase. [refseq;acc:nm_152230] Squared 22271.9 25656.8 1.15198
NETO2 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Rooted 52.9804 50.0947 1.0576
PPP2R5A serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Ranked 130.066 134.527 1.0343
965 AFG3L2 afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] Squared 22271.9 25656.8 1.15198

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/