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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2651 to 2700 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    1326 CSMD1 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] High confidence 218.509 1.02275 213.648
    DHX38 pre-mrna splicing factor atp-dependent rna helicase prp16 (atp- dependent rna helicase ddx38) (deah-box protein 38). [swissprot;acc:q92620] Low confidence 202.039 1.02219 197.654
    1327 DNAJB5 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] 201.908 197.525
    ZIC4 zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] High confidence 218.509 1.02275 213.648
    1328 no value 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Low confidence 198.342 1.02218 194.038
    RCAN2 calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] High confidence 218.509 1.02275 213.649
    1329 no value dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] 213.648
    CPA1 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Low confidence 187.586 1.02218 183.516
    1330 MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 152.998 1.02217 156.39
    RCAN1 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] High confidence 218.508 1.02275 213.648
    1331 RAB11A ras-related protein rab-11a (rab-11) (24kg) (yl8). [swissprot;acc:p24410] Low confidence 203.955 1.02217 199.531
    RCAN3 calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] High confidence 218.509 1.02275 213.649
    1332 LRPAP1 alpha-2-macroglobulin receptor-associated protein precursor (alpha-2-mrap) (low density lipoprotein receptor-related protein- associated protein 1) (rap). [swissprot;acc:p30533] Low confidence 203.765 1.02215 199.349
    OXA1L cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] High confidence 220.681 1.02271 215.78
    1333 MCM6 dna replication licensing factor mcm6 (p105mcm). [swissprot;acc:q14566] Low confidence 202.379 1.02215 197.993
    MRPL34 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] High confidence 220.681 1.02271 215.78
    1334 MCM10 minichromosome maintenance protein 10 isoform 2; homolog of yeast mcm10. [refseq;acc:nm_018518] Low confidence 202.379 1.02215 197.993
    PRAF2 jm4 protein. [refseq;acc:nm_007213] High confidence 199.643 1.02264 204.163
    1335 ARL6IP5 cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [refseq;acc:nm_006407] 199.771 1.02261 204.287
    CYB5R1 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Low confidence 200.614 1.02214 196.269
    1336 ERCC5 dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] 207.328 202.837
    GALK2 n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] High confidence 215.162 1.02257 210.412
    1337 no value galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902]
    CYB5R3 nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Low confidence 200.614 1.02214 196.269
    1338 DLAT dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [swissprot;acc:p10515] 204.159 1.02213 199.739
    GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] High confidence 215.162 1.02257 210.412
    1339 CEPT1 choline/ethanolaminephosphotransferase. [refseq;acc:nm_006090] Low confidence 187.632 1.02213 183.57
    NPC2 epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] High confidence 205.204 1.02239 200.71
    1340 SUV39H2 histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] 226.433 1.02234 231.491
    TBC1D5 tbc1 domain family member 5. [swissprot;acc:q92609] Low confidence 203.872 1.02213 199.458
    1341 EIF2S1 eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] High confidence 226.433 1.02234 231.491
    RECK reversion-inducing cysteine-rich protein with kazal motifs precursor (hreck) (suppressor of tumorigenicity 15) (st15). [swissprot;acc:o95980] Low confidence 187.632 1.02213 183.57
    1342 CHPT1 choline phosphotransferase 1; cholinephosphotransferase 1 alpha; cholinephosphotransferase 1. [refseq;acc:nm_020244] 187.631 183.569
    SUV39H1 histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463] High confidence 226.433 1.02234 231.491
    1343 CDC25A m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] 258.558 1.02231 252.916
    MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Low confidence 153.029 1.02213 156.416
    1344 CSNK2A2 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 204.058 199.639
    EXO1 exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] High confidence 216.772 1.02224 221.594
    1345 ESD esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Low confidence 200.431 1.02212 196.093
    FANCL phd finger protein 9. [refseq;acc:nm_018062] High confidence 216.772 1.02224 221.594
    1346 SOLH small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632]
    VPS35 vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Low confidence 201.165 1.02212 196.812
    1347 LIAS lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] High confidence 204.961 1.02223 209.517
    MRPL24 mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] Low confidence 205.323 1.02211 200.881
    1348 PPIF peptidyl-prolyl cis-trans isomerase, mitochondrial precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin f). [swissprot;acc:p30405] 201.458 197.1
    ZIC1 zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] High confidence 218.569 1.02215 213.832
    1349 CPA5 carboxypeptidase a5. [refseq;acc:nm_080385] Low confidence 187.671 1.0221 183.613
    ZIC3 zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] High confidence 218.572 1.02212 213.841
    1350 CCT8 t-complex protein 1, theta subunit (tcp-1-theta) (cct-theta). [swissprot;acc:p50990] Low confidence 201.762 1.0221 197.399
    ZIC2 zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] High confidence 218.574 213.847

    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/