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 Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1280 to 1329 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    320 RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Measured 20911 24908.5 1.19117
    321 no value c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Ranked 241.892 265.959 1.09949
    u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Rooted 55.9231 62.0565 1.10968
    NME2P1 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Squared 33526 42390.2 1.2644
    RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Measured 20911 24908.5 1.19117
    322 ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
    DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Ranked 86.7483 78.8995 1.09948
    GIPC1 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Rooted 60.594 67.2244 1.10942
    NME2 nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Squared 33522.8 42384.8 1.26436
    323 no value 60s ribosomal protein l23a. [swissprot;acc:p29316] Ranked 241.884 265.945 1.09947
    nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Squared 33514.4 42370.8 1.26426
    LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Measured 4620.76 5501.94 1.1907
    PCYT1A cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Rooted 50.3803 45.4193 1.10923
    324 DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Measured 28136.5 33457.6 1.18912
    FLAD1 fad synthetase. [refseq;acc:nm_025207] Rooted 50.3803 45.4193 1.10923
    HARS2 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Squared 34527.9 43507.9 1.26008
    RPS23 40s ribosomal protein s23. [swissprot;acc:p39028] Ranked 243.944 268.195 1.09941
    325 no value bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Rooted 50.3803 45.4193 1.10923
    HARS histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Squared 34506.3 43476 1.25994
    MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Ranked 243.944 268.195 1.09941
    SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured 16177.9 19235.4 1.18899
    326 ANAPC2 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] Squared 69124.3 54897.4 1.25915
    DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Measured 3432.96 4081.21 1.18883
    LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Rooted 50.3803 45.4193 1.10923
    RPL5 60s ribosomal protein l5. [swissprot;acc:p46777] Ranked 241.899 265.924 1.09932
    327 LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Squared 16424.1 20645.8 1.25704
    PAPSS1 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Rooted 50.3803 45.4193 1.10923
    POLR2A dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Ranked 243.817 267.962 1.09903
    SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Measured 16067.4 19094.4 1.18839
    328 BRP44 brain protein 44. [swissprot;acc:o95563] 15999.1 19007.1 1.18801
    DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Ranked 258.437 235.183 1.09888
    LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Squared 16442.8 20662.7 1.25664
    POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Rooted 50.3803 45.4193 1.10923
    329 MTX2 metaxin 2. [swissprot;acc:o75431] Squared 41236 51807 1.25635
    NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Ranked 312 284 1.09859
    PCYT1B cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Rooted 50.3803 45.4193 1.10923
    SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Measured 15999.1 19007.1 1.18801
    330 CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Ranked 312 284 1.09859
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Squared 16203.4 20339.9 1.25529
    SEPT6 septin 6. [swissprot;acc:q14141] Measured 15959.9 18957.1 1.1878
    SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] Rooted 50.519 45.5497 1.1091
    331 CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Ranked 312 284 1.09859
    PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Measured 20287.2 17083.8 1.18751
    RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Squared 33100.3 41520.6 1.25439
    SHROOM2 apical-like protein (apxl protein). [swissprot;acc:q13796] Rooted 60.6697 67.2802 1.10896
    332 NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Ranked 312 284 1.09859
    NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Squared 14464.3 18142.8 1.25432
    PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Measured 5051.16 5975.51 1.183
    SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Rooted 60.6732 67.2827 1.10894
    333 GTPBP4 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 49.0526 54.3781 1.10857

    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/