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 [...,...].
    Network Comparison Type Rank Gene Value Type description Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 1675 to 1724 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    210 Ranked cullin homolog 2 (cul-2). [swissprot;acc:q13617] CUL2 High confidence 1.13261 285.684 252.234
    dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] FMO2 Low confidence 1.05016 209.782 199.761
    Squared hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] HEY2 1.10746 52137.6 47078.4
    small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] SGTA High confidence 1.33652 69549 92953.5
    Rooted alpha crystallin a chain. [swissprot;acc:p02489] CRYAA Low confidence 1.06027 65.7815 69.7461
    calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] CAPN1 High confidence 1.14256 46.8525 53.5316
    211 Measured bet3 homolog. [swissprot;acc:o43617] TRAPPC3 Low confidence 1.07119 8749.42 9372.33
    voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] CACNG4 High confidence 1.24905 4068.91 5082.27
    Ranked dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] FMO1 Low confidence 1.05012 209.768 199.756
    presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] PSEN1 High confidence 1.13261 285.684 252.234
    Squared fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] FIP1L1 Low confidence 1.10705 51856.6 46842.3
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 High confidence 1.3326 14668.3 19547
    Rooted alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] CRYAB Low confidence 1.06018 65.7981 69.7576
    metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] PITRM1 High confidence 1.14095 88.4361 77.5112
    212 Measured tbp-associated factor 2; taf2 rna polymerase ii, tata box binding protein (tbp)-associated factor, 150 kd; tata box binding protein (tbp)-associated factor, rna polymerase ii, b, 150kd; cofactor of initiator function, 150kd subunit. [refseq;acc:nm_003184] TAF2 Low confidence 1.07104 6236.57 6679.63
    transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] BRF1 High confidence 1.24896 4446.72 5553.79
    Ranked cullin homolog 1 (cul-1). [swissprot;acc:q13616] CUL1 1.13261 285.684 252.234
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] GNG11 Low confidence 1.05011 211.383 221.976
    Squared cdc14 homolog a isoform 1. [refseq;acc:nm_003672] CDC14A 1.10702 53620.1 48436.6
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] TIAL1 High confidence 1.3315 14690.3 19560.2
    Rooted beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] ALG1 1.14092 88.4266 77.5047
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] SNRPD1 Low confidence 1.05988 71.0886 75.3451
    213 Measured nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] NOLA1 High confidence 1.24896 4446.72 5553.79
    putative alpha-mannosidase c20orf31 precursor (ec 3.2.1.-). [swissprot;acc:q9bv94] EDEM2 Low confidence 1.07056 7777.65 8326.47
    Ranked dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] FMO4 1.05011 209.765 199.755
    pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] PLDN High confidence 1.127 210.693 186.95
    Squared cyclin a1. [swissprot;acc:p78396] CCNA1 Low confidence 1.10638 62221.2 56238.4
    signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] STAM High confidence 1.32877 86861.5 65369.7
    Rooted asc-type amino acid transporter 1 (asc-1). [swissprot;acc:q9ns82] SLC7A10 Low confidence 1.05987 67.8941 71.9592
    associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] STAMBPL1 High confidence 1.14054 105.205 92.2415
    214 Measured core1 udp-galactose:n-acetylgalactosamine-alpha-r beta 1,3-galac. [refseq;acc:nm_020156] C1GALT1 Low confidence 1.07014 10492.4 9804.73
    voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] CACNG5 High confidence 1.24827 4074.83 5086.49
    Ranked lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 1.12605 191.644 170.192
    udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] OGT Low confidence 1.05001 206.583 196.743
    Squared step ii splicing factor slu7. [refseq;acc:nm_006425] SLU7 1.10627 59126.8 65410.1
    trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] TRMU High confidence 1.32807 52591.3 69845.1
    Rooted putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] CHMP2A 1.14054 105.205 92.2415
    putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] FMO6P Low confidence 1.05982 69.3281 73.4756
    215 Measured neurochondrin. [refseq;acc:nm_014284] NCDN 1.07014 10492.4 9804.73
    transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] KRAS High confidence 1.24717 16074 12888.4
    Ranked a kindred of iglon. [refseq;acc:nm_173808] NEGR1 Low confidence 1.05 199.671 209.654
    myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] no value High confidence 1.125 112 126
    Squared lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] LIPA Low confidence 1.1056 54531.1 49322.8
    protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] PRKCH High confidence 1.32766 86609.4 65234.5
    Rooted associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] STAMBP 1.14054 105.205 92.2415
    dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] FMO3 Low confidence 1.05978 69.3328 73.4772
    216 Measured leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] SHOC2 High confidence 1.24714 16071.6 12886.8
    protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] PPP1R12A Low confidence 1.06962 8973.23 9597.94
    Ranked myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] MYH4 High confidence 1.125 112 126
    neuromedin-b receptor (nmb-r) (neuromedin-b-preferring bombesin receptor). [swissprot;acc:p28336] NMBR Low confidence 1.05 199.671 209.654

    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/