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 [...,...].
    Network Comparison Type Rank description Gene Value Type Hugo Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2625 to 2674 of 16578 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    1313 serologically defined colon cancer antigen 1. [refseq;acc:nm_004713] SDCCAG1 Low confidence 202.396 197.985 1.02228
    signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] STAT3 High confidence 222.573 227.75 1.02326
    1314 dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] DNAJB1 Low confidence 201.948 197.549 1.02227
    signal transducer and activator of transcription 4. [swissprot;acc:q14765] STAT4 High confidence 222.573 227.751 1.02326
    1315 ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] UBQLN4 Low confidence 206.697 202.196 1.02226
    signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224] STAT1 High confidence 222.574 227.752 1.02326
    1316 schwannomin interacting protein 1. [refseq;acc:nm_014575] SCHIP1 Low confidence 201.232 196.85 1.02226
    signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] STAT6 High confidence 222.569 227.739 1.02323
    1317 cbf1 interacting corepressor. [refseq;acc:nm_004882] no value Low confidence 203.649 199.217 1.02225
    centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] CENPJ High confidence 206.773 202.105 1.0231
    1318 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] GPATCH1 Low confidence 203.649 199.217 1.02225
    signal transducer and activator of transcription 5a. [swissprot;acc:p42229] STAT5A High confidence 222.546 227.673 1.02304
    1319 fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [swissprot;acc:p51648] ALDH3A2 Low confidence 208.606 213.247 1.02225
    glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] GYS1 High confidence 159.75 156.153 1.02304
    1320 mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] MAPK14 Low confidence 200.171 195.819 1.02222
    signal transducer and activator of transcription 5b. [swissprot;acc:p51692] STAT5B High confidence 222.544 227.667 1.02302
    1321 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] C16orf42 Low confidence 199.938 195.591 1.02222
    probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] DIMT1L High confidence 226.347 221.259 1.023
    1322 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] AGPAT2 Low confidence 198.322 194.014 1.0222
    endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] no value High confidence 159.86 156.275 1.02294
    1323 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] NCK2 205.225 200.625 1.02293
    neuronal guanine nucleotide exchange factor. [refseq;acc:nm_019850] NGEF Low confidence 203.926 199.498 1.0222
    1324 beta-galactosidase precursor (ec 3.2.1.23) (lactase) (acid beta- galactosidase). [swissprot;acc:p16278] GLB1 203.758 199.335 1.02219
    glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] GYS2 High confidence 159.993 156.421 1.02284
    1325 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] DNAJB4 Low confidence 201.909 197.526 1.02219
    werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] WRNIP1 High confidence 217.133 212.289 1.02282
    1326 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] CSMD1 218.509 213.648 1.02275
    pre-mrna splicing factor atp-dependent rna helicase prp16 (atp- dependent rna helicase ddx38) (deah-box protein 38). [swissprot;acc:q92620] DHX38 Low confidence 202.039 197.654 1.02219
    1327 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] DNAJB5 201.908 197.525
    zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] ZIC4 High confidence 218.509 213.648 1.02275
    1328 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] no value Low confidence 198.342 194.038 1.02218
    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] RCAN2 High confidence 218.509 213.649 1.02275
    1329 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] CPA1 Low confidence 187.586 183.516 1.02218
    dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] no value High confidence 218.509 213.648 1.02275
    1330 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] RCAN1 218.508
    microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] MAP1LC3B Low confidence 152.998 156.39 1.02217
    1331 calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] RCAN3 High confidence 218.509 213.649 1.02275
    ras-related protein rab-11a (rab-11) (24kg) (yl8). [swissprot;acc:p24410] RAB11A Low confidence 203.955 199.531 1.02217
    1332 alpha-2-macroglobulin receptor-associated protein precursor (alpha-2-mrap) (low density lipoprotein receptor-related protein- associated protein 1) (rap). [swissprot;acc:p30533] LRPAP1 203.765 199.349 1.02215
    cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] OXA1L High confidence 220.681 215.78 1.02271
    1333 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] MRPL34
    dna replication licensing factor mcm6 (p105mcm). [swissprot;acc:q14566] MCM6 Low confidence 202.379 197.993 1.02215
    1334 jm4 protein. [refseq;acc:nm_007213] PRAF2 High confidence 199.643 204.163 1.02264
    minichromosome maintenance protein 10 isoform 2; homolog of yeast mcm10. [refseq;acc:nm_018518] MCM10 Low confidence 202.379 197.993 1.02215
    1335 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] CYB5R1 200.614 196.269 1.02214
    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] ARL6IP5 High confidence 199.771 204.287 1.02261
    1336 dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] ERCC5 Low confidence 207.328 202.837 1.02214
    n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] GALK2 High confidence 215.162 210.412 1.02257
    1337 galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] no value
    nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] CYB5R3 Low confidence 200.614 196.269 1.02214

    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/