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 823 to 872 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    206 DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Squared 12326.4 16522.9 1.34045
    LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Ranked 228.085 201.006 1.13472
    207 no value splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Measured 4771.21 5961.43 1.24946
    ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Rooted 140.508 122.878 1.14348
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Ranked 285.684 252.234 1.13261
    SLC4A1AP solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Squared 70525.9 52678.7 1.33879
    208 CACNG8 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Measured 4068.78 5082.18 1.24907
    CKS2 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Squared 70525.9 52678.7 1.33879
    DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Rooted 46.901 53.624 1.14334
    SKP1A s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Ranked 285.684 252.234 1.13261
    209 CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Measured 4068.78 5082.18 1.24907
    CAPN2 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Rooted 46.8525 53.5324 1.14257
    CTNNAL1 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Squared 70525.9 52678.7 1.33879
    FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Ranked 285.684 252.234 1.13261
    210 CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Measured 4068.82 5082.21 1.24906
    CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Rooted 46.8525 53.5316 1.14256
    CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Ranked 285.684 252.234 1.13261
    SGTA small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Squared 69549 92953.5 1.33652
    211 CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Measured 4068.91 5082.27 1.24905
    PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Rooted 88.4361 77.5112 1.14095
    PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Ranked 285.684 252.234 1.13261
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Squared 14668.3 19547 1.3326
    212 ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Rooted 88.4266 77.5047 1.14092
    BRF1 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] Measured 4446.72 5553.79 1.24896
    CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Ranked 285.684 252.234 1.13261
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Squared 14690.3 19560.2 1.3315
    213 NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Measured 4446.72 5553.79 1.24896
    PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Ranked 210.693 186.95 1.127
    STAM signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Squared 86861.5 65369.7 1.32877
    STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Rooted 105.205 92.2415 1.14054
    214 CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Measured 4074.83 5086.49 1.24827
    CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Rooted 105.205 92.2415 1.14054
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Ranked 191.644 170.192 1.12605
    TRMU trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Squared 52591.3 69845.1 1.32807
    215 no value myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Ranked 112 126 1.125
    KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Measured 16074 12888.4 1.24717
    PRKCH protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Squared 86609.4 65234.5 1.32766
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Rooted 105.205 92.2415 1.14054
    216 MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Ranked 112 126 1.125
    PRKCE protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Squared 86600.9 65229.9 1.32763
    SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Measured 16071.6 12886.8 1.24714
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Rooted 105.205 92.2415 1.14054
    217 no value ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Measured 16071.6 12886.8 1.24714
    CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Rooted 105.205 92.2415 1.14054
    MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Ranked 112 126 1.125
    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] Squared 86600.9 65229.9 1.32763
    218 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Rooted 46.1476 52.5742 1.13926
    HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Measured 16070.4 12886 1.24712
    MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Ranked 112 126 1.125
    OGT udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Squared 86600.9 65229.9 1.32763

    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/