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 [...,...].
    Gene Hugo description Rank Value Type Interaction Map red green Network Comparison Type Filtered network_comparison
    Results: HTML CSV LaTeX Showing element 1 to 50 of 3228 in total
    Hugo  : no value
    Value Type  : Ranked
    Interaction Map  : High confidence
    Network Comparison Type  : Divided
    Filtered  : 1
    description
    		Rank
    		red
    		green
    		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 186.741 181.041 1.03148
    15 kda selenoprotein precursor. [swissprot;acc:o60613] 1948 214.522 212.432 1.00984
    17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] 1051 211.449 217.998 1.03097
    26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 2316 217.241 218.311 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 196.008 198.154 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 219.423 222.215 1.01272
    40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 304 242.339 266.986 1.1017
    40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 387 242.238 264.11 1.09029
    40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 344 241.625 265.136 1.0973
    40s ribosomal protein s26. [swissprot;acc:p02383] 454 210.224 226.578 1.07779
    40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 1102 229.442 235.974 1.02847
    40s ribosomal protein s28. [swissprot;acc:p25112] 1982 200.343 198.427 1.00966
    40s ribosomal protein s29. [swissprot;acc:p30054] 277 241.849 267.642 1.10665
    40s ribosomal protein s3a. [swissprot;acc:p49241] 867 225.689 234.674 1.03981
    40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 288 240.758 266.078 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] 789 224.244 234.511 1.04578
    60s acidic ribosomal protein p1. [swissprot;acc:p05386] 898 229.171 238.048 1.03874
    60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 357 243.12 266.661 1.09683
    60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 356 243.24 266.796 1.09684
    60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 338 243.583 267.528 1.0983
    60s ribosomal protein l12. [swissprot;acc:p30050] 337 267.527
    60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 306 242.153 266.673 1.10126
    60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 281 241.808 267.335 1.10557
    60s ribosomal protein l18a. [swissprot;acc:q02543] 860 234.025 224.958 1.04031
    60s ribosomal protein l21. [swissprot;acc:p46778] 1054 223.958 217.263 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 199.129 200.413 1.00645
    60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 293 240.782 265.717 1.10356
    60s ribosomal protein l23a. [swissprot;acc:p29316] 323 241.884 265.945 1.09947
    60s ribosomal protein l37a. [swissprot;acc:p12751] 2959 0.00001 0.00001 1
    60s ribosomal protein l39. [swissprot;acc:p02404] 859 234.025 224.958 1.04031
    60s ribosomal protein l7. [swissprot;acc:p18124] 297 235.727 259.984 1.1029
    60s ribosomal protein l9. [swissprot;acc:p32969] 341 240.243 263.798 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 215.799 213.865 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 222.134 225.731 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 199.928 198.24 1.00851
    adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 1049 211.449 217.998 1.03097
    adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 348 242.14 265.696 1.09728
    adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 1186 218.402 212.904 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 192.871 193.555 1.00355
    alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 1189 209.649 204.406 1.02565
    alpha-nac protein. [sptrembl;acc:q9h009] 889 212.028 204.053 1.03908
    alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 1249 219.354 224.7 1.02437
    apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 248 237.302 212.41 1.11719
    apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 1111 217.99 212.123 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 200.158 201.213 1.00527
    aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 658 229.072 216.576 1.0577
    ataxin 2-binding protein. [swissprot;acc:q9nwb1] 1704 218.514 215.577 1.01362
    ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 1059 228.105 221.293 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/