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 Value Type description Hugo Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2232 to 2281 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		red
    		network_comparison
    		green
    1116 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] SPTLC2 Subtracted 204.603 5.721 210.324
    1117 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] NXF5 Divided 168.989 1.02754 164.46
    steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] ESRRB Subtracted 186.551 5.714 180.837
    1118 epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] EPS8L2 221.877 5.71 216.167
    nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] NXF3 Divided 168.995 1.02753 164.467
    1119 peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] PRDX5 Subtracted 207.553 5.703 213.256
    vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] ATP6V0A2 Divided 218.528 1.02752 212.676
    1120 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 Subtracted 186.741 5.7 181.041
    atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] ATP6V0A4 Divided 218.528 1.02752 212.676
    1121 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 Subtracted 187.834 5.697 182.137
    vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] ATP6V0A1 Divided 218.529 1.02752 212.676
    1122 heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] HNRNPL Subtracted 186.774 5.675 181.099
    vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] TCIRG1 Divided 218.527 1.02751 212.676
    1123 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] no value Subtracted 186.799 5.672 181.127
    nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] NXF1 Divided 169.031 1.0275 164.507
    1124 kappa b-ras 1. [refseq;acc:nm_020345] no value Subtracted 220.758 5.661 215.097
    peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] PRDX5 Divided 207.553 1.02748 213.256
    1125 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] no value 204.404 210.022
    i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] NKIRAS2 Subtracted 220.758 5.661 215.097
    1126 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] ATP6V0D2 Divided 218.487 1.02742 212.656
    snare associated protein snapin. [refseq;acc:nm_012437] SNAPAP Subtracted 220.758 5.661 215.097
    1127 nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] no value Divided 239.219 1.02741 232.837
    sorting nexin 1. [swissprot;acc:q13596] SNX1 Subtracted 209.868 5.654 215.522
    1128 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 5.652 182.308
    homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] SIX1 Divided 221.286 1.02733 215.399
    1129 homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] SIX2 221.285 1.02732 215.401
    m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] CDC25A Subtracted 258.558 5.642 252.916
    1130 proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] PA2G4 Divided 221.285 1.02732 215.4
    steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] ESRRA Subtracted 187.022 5.631 181.391
    1131 transducin-like enhancer protein 4. [swissprot;acc:q04727] TLE4 219.438 5.62 213.818
    vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] no value Divided 218.484 1.02731 212.675
    1132 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] API5
    folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] FPGS Subtracted 225.906 5.618 231.524
    1133 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] no value 204.404 210.022
    sec13-related protein. [swissprot;acc:p55735] SEC13 Divided 218.484 1.02731 212.675
    1134 transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] TLE3 Subtracted 219.401 5.616 213.785
    vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] ATP6V1G3 Divided 218.484 1.02731 212.675
    1135 homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] EN2 Subtracted 219.399 5.615 213.784
    vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] ATP6V1B2 Divided 218.484 1.02731 212.675
    1136 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] CXXC1 Subtracted 219.399 5.615 213.784
    yeast sec31p homolog. [refseq;acc:nm_014933] SEC31A Divided 218.484 1.02731 212.675
    1137 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] ABT1 Subtracted 219.399 5.615 213.784
    vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] ATP6V1G1 Divided 218.484 1.02731 212.675
    1138 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] no value Subtracted 219.399 5.615 213.784
    vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] ATP6V1E1 Divided 218.484 1.02731 212.675
    1139 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] GDAP1L1
    transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] TLE2 Subtracted 219.374 5.615 213.759
    1140 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] DDX39 Divided 218.484 1.02731 212.675
    hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] HECW1 Subtracted 219.399 5.615 213.784
    1141 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] GDAP1 Divided 218.484 1.02731 212.675

    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/