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 red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 2580 to 2629 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		green
    		network_comparison
    323 HNRNPL heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Measured Subtracted 10247.8 11289 1041.2
    LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Divided 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
    PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Subtracted 125.493 117.944 7.549
    RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Ranked 242.238 264.11 21.872
    324 no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
    CPB2 plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Squared 25326.2 18354.1 6972.1
    DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Measured Divided 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
    PPP1R2P9 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Rooted Subtracted 125.447 117.906 7.541
    PRKCH protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Measured 11773.7 10733.8 1039.9
    RPS23 40s ribosomal protein s23. [swissprot;acc:p39028] Ranked Divided 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
    myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Squared Subtracted 19321 12542.6 6778.4
    GORASP2 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Measured 8362.81 9402.7 1039.89
    HARS histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Squared Divided 34506.3 43476 1.25994
    MRPL13 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Ranked Subtracted 241.828 263.62 21.792
    MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Divided 243.944 268.195 1.09941
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Rooted Subtracted 100.684 108.135 7.451
    SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured Divided 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
    LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Subtracted 56.0466 63.4808 7.4342
    MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Squared 19321 12542.6 6778.4
    PRKCE protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Measured 11773 10733.2 1039.8
    RPL5 60s ribosomal protein l5. [swissprot;acc:p46777] Ranked Divided 241.899 265.924 1.09932
    RPS16 40s ribosomal protein s16. [swissprot;acc:p17008] Subtracted 241.828 263.62 21.792
    327 LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Squared Divided 16424.1 20645.8 1.25704
    MAX max protein. [swissprot;acc:p25912] Rooted Subtracted 56.3054 63.7148 7.4094
    MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Squared 19321 12542.6 6778.4
    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 Divided 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
    PPIB peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Measured Subtracted 11773 10733.2 1039.8
    RPL13A 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Ranked 241.83 263.615 21.785
    SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Measured Divided 16067.4 19094.4 1.18839
    328 no value putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Ranked Subtracted 240.801 262.34 21.539
    BRP44 brain protein 44. [swissprot;acc:o95563] Measured Divided 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
    MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Subtracted 19321 12542.6 6778.4
    OGT udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Measured 11773 10733.2 1039.8
    POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Rooted Divided 50.3803 45.4193 1.10923
    RRS1 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Subtracted 124.41 117.043 7.367
    329 COX4I1 cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] Measured 11773 10733.2 1039.8
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Ranked 191.644 170.192 21.452
    MTX2 metaxin 2. [swissprot;acc:o75431] Squared Divided 41236 51807 1.25635
    MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Subtracted 19321 12542.6 6778.4
    NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Ranked Divided 312 284 1.09859

    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/