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 description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2708 to 2757 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		network_comparison
    		green
    2708 porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] HMBS 227.796 1.0006 227.66
    2709 importin 7; ran-binding protein 7. [refseq;acc:nm_006391] no value 220.521 1.00057 220.395
    2710 importin 8; ran-binding protein 8. [refseq;acc:nm_006390] IPO8
    2711 brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] ARFGEF2
    2712 hsgcn1 (fragment). [sptrembl;acc:q99736] GCN1L1
    2713 brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] ARFGEF1
    2714 similar to trna synthetase class ii. [refseq;acc:nm_152268] PARS2 220.224 1.00056 220.348
    2715 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] no value 216.018 1.00053 215.903
    2716 salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162] PRB4
    2717 microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] MAPRE2 216.521 1.00052 216.634
    2718 histidine-rich membrane protein ke4. [swissprot;acc:q92504] SLC39A7 216.52 216.632
    2719 microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691] MAPRE1
    2720 microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8] MAPRE3 216.633
    2721 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] EPRS 221.022 1.00043 221.116
    2722 transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] TBL2 219.308 219.214
    2723 lamin b2. [swissprot;acc:q03252] no value 219.323 1.00041 219.413
    2724 heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238] HSP90AB1 221.053 220.963
    2725 doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] DCX 216.496 1.00034 216.569
    2726 rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873] RAD17 221.001 1.00033 220.927
    2727 atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] no value
    2728 atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010] XRCC5
    2729 ubiquitin-specific protease otubain 1. [refseq;acc:nm_017670] OTUB1 202.123 1.00031 202.06
    2730 complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021] C1QBP 212.922 1.0003 212.985
    2731 sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238] SIRT1
    2732 general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830] GCN5L2 202.233 1.00029 202.175
    2733 p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831] PCAF 202.229 1.00028 202.172
    2734 ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] no value 219.95 1.00026 220.007
    2735 heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900] HSP90AA2 220.943 1.00025 220.887
    2736 transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] no value 198.278 1.00022 198.321
    2737 transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9] MAFF
    2738 transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] no value
    2739 cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] CHL1
    2740 neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] no value
    2741 transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] TAF9
    2742 nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [swissprot;acc:q14494] NFE2L1
    2743 nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] NFE2L3
    2744 transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354] TADA3L 201.476 1.00019 201.514
    2745 frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331] FRG1
    2746 transcriptional adapter 2-like (ada2-like protein) (kl04p). [swissprot;acc:o75478] TADA2L
    2747 bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] BRD7 201.477 1.00018
    2748 small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] SGTA 189.563 1.00017 189.531
    2749 hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] HGS 190.522 1.00014 190.496
    2750 conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] COG7
    2751 proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [swissprot;acc:p25786] PSMA1 215.338 1.00012 215.312
    2752 p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44] TP53RK 221.7 1.00007 221.716
    2753 serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] AGXT 208.859 1.00006 208.846
    2754 5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] MTHFS 210.638 1.00002 210.642
    2755 deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] DHPS 212.403 1.00001 212.401
    2756 3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] no value 0.00001 1 0.00001
    2757 nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209] NAP1L1

    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/