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 [...,...].
    description Rank Gene Hugo Value Type Network Comparison Type red Interaction Map Filtered network_comparison green
    Results: HTML CSV LaTeX Showing element 236 to 285 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    af-6 protein. [swissprot;acc:p55196] 1530 MLLT4 218.733 1.01746 214.98
    afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] 1725 AFG3L2 217.676 1.01311 220.53
    aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] 1969 AKR7A2 211.633 1.00978 213.703
    aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] 1958 AKR7A3
    ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] 1157 AIP 224.307 1.02646 230.242
    alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 2025 GPT 189.987 1.00885 191.668
    alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443] 2030 GPT2 189.999 1.00883 191.677
    alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] 633 AARS 234.106 1.05979 248.104
    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 no value 192.871 1.00355 193.555
    aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353] 3222 ALDH3B1 0.00001 1 0.00001
    aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] 2992 ALDH3B2
    aldehyde oxidase (ec 1.2.3.1). [swissprot;acc:q06278] 2960 AOX1
    alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] 1965 ADD1 224.432 1.00978 222.258
    alpha crystallin a chain. [swissprot;acc:p02489] 2875 CRYAA 0.00001 1 0.00001
    alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] 3082 CRYAB
    alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] 1450 HSPB8 221.804 1.01979 226.194
    alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] 2363 ENO1 207.186 1.00415 208.046
    alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5] 1726 FUT8 217.676 1.01311 220.53
    alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 1189 no value 209.649 1.02565 204.406
    alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424] 2587 SNTA1 213.422 1.00154 213.75
    alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] 1806 ACTN1 217.009 1.01178 214.482
    alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] 1799 ACTN2 217.016 1.01182 214.481
    alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] 1805 ACTN4 217.008 1.01178 214.482
    alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] 1509 ACTR1A 225.148 1.01795 221.177
    alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911] 2255 ZFHX3 202.366 1.00595 203.57
    alpha-nac protein. [sptrembl;acc:q9h009] 889 no value 212.028 1.03908 204.053
    alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 1249 219.354 1.02437 224.7
    alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920] 812 NAPA 212.386 1.04425 221.785
    alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870] 1961 ABHD1 211.633 1.00978 213.703
    alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] 1959 ABHD3
    alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [refseq;acc:nm_024083] 2829 ASPSCR1 0.00001 1 0.00001
    amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] 637 PPAT 228.639 1.05957 242.258
    aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] 1420 ACY1 203.979 1.02084 208.229
    aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] 2064 AASS 207.655 1.00833 205.939
    aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] 2544 AMT 212.67 1.00192 212.262
    ammecr1 protein. [refseq;acc:nm_015365] 1577 AMMECR1 222.585 1.01645 218.982
    amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 52 AMPD2 133 1.26667 105
    amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] 139 APBA1 271.752 1.20415 225.68
    amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] 2490 APPBP1 194.527 1.00284 195.08
    amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [refseq;acc:nm_006380] 3191 APPBP2 0.00001 1 0.00001
    anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] 2636 ANAPC11 195.635 1.00128 195.384
    anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] 2663 ANAPC10 204.768 1.00107 204.549
    anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] 2679 ANAPC2 190.142 1.00096 189.959
    androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 240 AIG1 227.357 1.11785 254.15
    angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201] 2586 AMOTL2 213.422 1.00154 213.75
    angiomotin. [refseq;acc:nm_133265] 2585 AMOT
    anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 143 ANLN 59 1.20408 49
    ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484] 2519 ANK2 215.835 1.00234 216.341
    ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955] 2518 ANK3
    ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] 805 ANKRA2 212.386 1.04425 221.785

    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/