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 Network Comparison Type Gene Hugo Value Type description Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2201 to 2250 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		red
    		network_comparison
    		green
    1101 Divided KARS lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] 220.291 1.02857 226.584
    Subtracted GDAP1L1 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] 218.484 5.809 212.675
    1102 Divided no value 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 229.442 1.02847 235.974
    Subtracted DDX39 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] 218.484 5.809 212.675
    1103 Divided RPS27L ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] 229.441 1.02846 235.972
    Subtracted GDAP1 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 218.484 5.809 212.675
    1104 Divided HAO1 hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] 231.922 1.0283 238.486
    Subtracted ATP6V1D vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] 218.484 5.809 212.675
    1105 Divided FDX1 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 191.139 1.02828 185.882
    Subtracted SEC31B secretory pathway component sec31b-1. [refseq;acc:nm_015490] 218.484 5.809 212.675
    1106 Divided PEX5L pxr2b protein. [refseq;acc:nm_016559] 212.945 1.02818 207.109
    Subtracted ATP6V1H vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] 218.484 5.809 212.675
    1107 Divided 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] 204.603 1.02796 210.324
    Subtracted ATP6V1B1 vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] 218.483 5.807 212.676
    1108 Divided FOXK2 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 218.006 1.02775 212.119
    Subtracted ATP6V1F vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] 218.481 5.806 212.675
    1109 Divided TPT1 translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] 218.098 1.02775 212.209
    Subtracted EPS8L1 epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] 221.939 5.796 216.143
    1110 Divided GIT2 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 216.78 1.02769 222.782
    Subtracted BHLHB4 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 159.13 5.787 164.917
    1111 Divided no value apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 217.99 1.02766 212.123
    Subtracted BHLHB5 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] 159.165 5.786 164.951
    1112 Divided HNF4G hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] 251.863 1.02766 258.829
    Subtracted EPS8 epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] 221.93 5.784 216.146
    1113 Divided GADD45G growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] 251.863 1.02766 258.829
    Subtracted PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 91.63 5.7711 97.4011
    1114 Divided GADD45A growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522] 251.863 1.02766 258.829
    Subtracted DPH2 diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384] 227.274 5.767 233.041
    1115 Divided HNF4A hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235] 251.863 1.02766 258.829
    Subtracted AGPAT2 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] 186.664 5.721 180.943
    1116 Divided GADD45B growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293] 251.863 1.02766 258.829
    Subtracted 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] 204.603 5.721 210.324
    1117 Divided NXF5 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 168.989 1.02754 164.46
    Subtracted ESRRB steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] 186.551 5.714 180.837
    1118 Divided NXF3 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 168.995 1.02753 164.467
    Subtracted EPS8L2 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] 221.877 5.71 216.167
    1119 Divided ATP6V0A2 vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] 218.528 1.02752 212.676
    Subtracted PRDX5 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] 207.553 5.703 213.256
    1120 Divided ATP6V0A4 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] 218.528 1.02752 212.676
    Subtracted 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] 186.741 5.7 181.041
    1121 Divided ATP6V0A1 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] 218.529 1.02752 212.676
    Subtracted AGPAT3 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] 187.834 5.697 182.137
    1122 Divided TCIRG1 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] 218.527 1.02751 212.676
    Subtracted HNRNPL heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] 186.774 5.675 181.099
    1123 Divided NXF1 nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 169.031 1.0275 164.507
    Subtracted no value estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 186.799 5.672 181.127
    1124 Divided PRDX5 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] 207.553 1.02748 213.256
    Subtracted no value kappa b-ras 1. [refseq;acc:nm_020345] 220.758 5.661 215.097
    1125 Divided dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 204.404 1.02748 210.022
    Subtracted NKIRAS2 i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] 220.758 5.661 215.097

    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/