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 [...,...].
    Hugo Gene description Interaction Map Rank Value Type green red Network Comparison Type Filtered network_comparison
    Results: HTML CSV LaTeX Showing element 1 to 50 of 3228 in total
    Hugo  : no value
    Interaction Map  : High confidence
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    description
    		Rank
    		green
    		red
    		network_comparison
    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] 1038 181.041 186.741 1.03148
    15 kda selenoprotein precursor. [swissprot;acc:o60613] 1948 212.432 214.522 1.00984
    17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] 1051 217.998 211.449 1.03097
    26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 2316 218.311 217.241 1.00493
    3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 2756 0.00001 0.00001 1
    3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060] 2802
    3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 1852 198.154 196.008 1.01095
    4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 1745 222.215 219.423 1.01272
    40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 304 266.986 242.339 1.1017
    40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 387 264.11 242.238 1.09029
    40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 344 265.136 241.625 1.0973
    40s ribosomal protein s26. [swissprot;acc:p02383] 454 226.578 210.224 1.07779
    40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 1102 235.974 229.442 1.02847
    40s ribosomal protein s28. [swissprot;acc:p25112] 1982 198.427 200.343 1.00966
    40s ribosomal protein s29. [swissprot;acc:p30054] 277 267.642 241.849 1.10665
    40s ribosomal protein s3a. [swissprot;acc:p49241] 867 234.674 225.689 1.03981
    40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 288 266.078 240.758 1.10517
    40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 789 234.511 224.244 1.04578
    60s acidic ribosomal protein p1. [swissprot;acc:p05386] 898 238.048 229.171 1.03874
    60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 357 266.661 243.12 1.09683
    60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 356 266.796 243.24 1.09684
    60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 338 267.528 243.583 1.0983
    60s ribosomal protein l12. [swissprot;acc:p30050] 337 267.527
    60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 306 266.673 242.153 1.10126
    60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 281 267.335 241.808 1.10557
    60s ribosomal protein l18a. [swissprot;acc:q02543] 860 224.958 234.025 1.04031
    60s ribosomal protein l21. [swissprot;acc:p46778] 1054 217.263 223.958 1.03082
    60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 2205 200.413 199.129 1.00645
    60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 293 265.717 240.782 1.10356
    60s ribosomal protein l23a. [swissprot;acc:p29316] 323 265.945 241.884 1.09947
    60s ribosomal protein l37a. [swissprot;acc:p12751] 2959 0.00001 0.00001 1
    60s ribosomal protein l39. [swissprot;acc:p02404] 859 224.958 234.025 1.04031
    60s ribosomal protein l7. [swissprot;acc:p18124] 297 259.984 235.727 1.1029
    60s ribosomal protein l9. [swissprot;acc:p32969] 341 263.798 240.243 1.09805
    acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] 2019 213.865 215.799 1.00904
    adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 1595 225.731 222.134 1.01619
    adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367] 2046 198.24 199.928 1.00851
    adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 1049 217.998 211.449 1.03097
    adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 348 265.696 242.14 1.09728
    adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 1186 212.904 218.402 1.02582
    alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 2428 193.555 192.871 1.00355
    alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 1189 204.406 209.649 1.02565
    alpha-nac protein. [sptrembl;acc:q9h009] 889 204.053 212.028 1.03908
    alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 1249 224.7 219.354 1.02437
    apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 248 212.41 237.302 1.11719
    apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 1111 212.123 217.99 1.02766
    arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] 2291 201.213 200.158 1.00527
    aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 658 216.576 229.072 1.0577
    ataxin 2-binding protein. [swissprot;acc:q9nwb1] 1704 215.577 218.514 1.01362
    ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 1059 221.293 228.105 1.03078

    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/