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 description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2051 to 2100 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    1026 gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] SGCG Low confidence 206.781 201.874 1.02431
    transforming protein rhoa (h12). [swissprot;acc:p06749] RHOA High confidence 205.632 199.266 1.03195
    1027 protein cgi-147. [swissprot;acc:q9y3e5] PTRH2 Low confidence 203.643 198.811 1.0243
    succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] SUCLG1 High confidence 211.908 218.627 1.03171
    1028 splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] SFRS8 Low confidence 203.574 198.744 1.0243
    succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7] SUCLA2 High confidence 211.908 218.627 1.03171
    1029 apical-like protein (apxl protein). [swissprot;acc:q13796] SHROOM2 Low confidence 204.847 199.989 1.02429
    dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] DDB1 High confidence 222.364 215.535 1.03168
    1030 nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] no value Low confidence 201.043 196.276 1.02429
    propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] PCCB High confidence 222.364 215.535 1.03168
    1031 probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] EMG1 242.978 235.518 1.03167
    thromboxane-a synthase (ec 5.3.99.5) (txa synthase) (txs). [swissprot;acc:p24557] TBXAS1 Low confidence 203.998 199.161 1.02429
    1032 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 High confidence 186.664 180.943 1.03162
    sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] SH3GL1 Low confidence 203.946 199.111 1.02428
    1033 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] SEPT4 172.447 168.363 1.02426
    tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] TYR High confidence 221.183 214.406 1.03161
    1034 multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] no value Low confidence 202.723 197.922 1.02426
    steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] ESRRB High confidence 186.551 180.837 1.0316
    1035 atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] MAGI2 221.682 228.68 1.03157
    nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209] NAP1L1 Low confidence 201.037 196.277 1.02425
    1036 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] COPB1 High confidence 171.341 176.746 1.03155
    ras-related protein rab-7. [swissprot;acc:p51149] RAB7A Low confidence 199.336 194.616 1.02425
    1037 l-3-phosphoserine phosphatase (ec 3.1.3.3) (psp) (o-phosphoserine phosphohydrolase) (pspase). [swissprot;acc:p78330] PSPHL 195.067 190.451 1.02424
    thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] GLRX3 High confidence 228.412 235.609 1.03151
    1038 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 186.741 181.041 1.03148
    block of proliferation 1. [swissprot;acc:q14137] BOP1 Low confidence 201.77 196.996 1.02423
    1039 dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] DLD High confidence 207.719 214.236 1.03137
    hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] HIF3A Low confidence 203.911 199.088 1.02423
    1040 brain protein 44. [swissprot;acc:o95563] BRP44 182.902 178.58 1.0242
    t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] CCT5 High confidence 163.24 168.359 1.03136
    1041 heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] HNRNPL 186.774 181.099 1.03134
    protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] C20orf4 Low confidence 200.541 195.802 1.0242
    1042 aspartate aminotransferase, cytoplasmic (ec 2.6.1.1) (transaminase a) (glutamate oxaloacetate transaminase-1). [swissprot;acc:p17174] GOT1 203.079 198.289 1.02416
    estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] no value High confidence 186.799 181.127 1.03132
    1043 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] AGPAT3 187.834 182.137 1.03128
    heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] HNRNPU Low confidence 210.83 205.858 1.02415
    1044 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] HRSP12 201.723 196.966
    t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] DYNLT3 High confidence 173.475 178.889 1.03121
    1045 aspartate aminotransferase, mitochondrial precursor (ec 2.6.1.1) (transaminase a) (glutamate oxaloacetate transaminase-2). [swissprot;acc:p00505] GOT2 Low confidence 203.088 198.3 1.02415
    fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] FIP1L1 High confidence 115.817 119.432 1.03121
    1046 double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] MRE11A 173.475 178.889
    red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] ACP1 Low confidence 201.208 196.467 1.02413
    1047 splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] SFRS11 205.265 200.428
    steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] ESRRA High confidence 187.022 181.391 1.03104
    1048 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] AGPAT4 187.96 182.308 1.031
    nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] RRP1 Low confidence 202.477 197.709 1.02412
    1049 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] no value High confidence 211.449 217.998 1.03097
    ubiquitin-conjugating enzyme e2 m (ec 6.3.2.19) (ubiquitin-protein ligase m) (ubiquitin carrier protein m) (nedd8-conjugating enzyme ubc12). [swissprot;acc:o76069] UBE2M Low confidence 198.569 193.893 1.02412
    1050 estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] HSD17B1 High confidence 211.449 217.998 1.03097
    protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] PPP1R12A Low confidence 194.002 189.435 1.02411

    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/