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 [...,...].
    Gene Rank Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1062 to 1111 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		Value Type
    		red
    		green
    		network_comparison
    133 PRSS16 Subtracted thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Squared 71062.2 95488.6 24426.4
    TMEM132A Divided gbp protein isoform a. [refseq;acc:nm_017870] 1182.25 1726.55 1.46039
    TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Ranked 350 290 1.2069
    134 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Measured 21785.2 16426.1 1.32626
    Subtracted huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Ranked 226.884 194.79 32.094
    CCDC47 gk001 protein. [refseq;acc:nm_020198] Squared 71062.2 95488.6 24426.4
    CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Measured 12796.8 10886 1910.8
    DAB2IP Divided dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Ranked 350 290 1.2069
    GATAD2A p66 alpha. [refseq;acc:nm_017660] Squared 81888.8 56306.5 1.45434
    POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Rooted 44.849 54.7964 1.2218
    SNRPD1 Subtracted small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 54.8203 67.934 13.1137
    135 ATG3 Divided apg3p; pc3-96 protein. [refseq;acc:nm_022488] Measured 21785.2 16426.1 1.32626
    CACNG8 Subtracted voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Rooted 49.2923 62.3969 13.1046
    CLSTN2 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Squared 71033.4 95440.2 24406.8
    CPEB4 Divided cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Ranked 350 290 1.2069
    FOXP4 Subtracted forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 263.215 231.407 31.808
    GATAD2B Divided transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Squared 81888.8 56306.5 1.45434
    JUNB Subtracted transcription factor jun-b. [swissprot;acc:p17275] Measured 5579.18 7488.4 1909.22
    NCBP2 Divided 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Rooted 54.935 66.6101 1.21253
    136 no value tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Squared 81888.8 56306.5 1.45434
    ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Rooted 41.8357 50.6469 1.21061
    CACNG3 Subtracted voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 49.2923 62.3969 13.1046
    CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Measured 12787.6 10880.5 1907.1
    CLSTN3 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Squared 71030.1 95434.8 24404.7
    CPEB3 Divided cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Ranked 350 290 1.2069
    FOXP1 Subtracted forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 263.215 231.407 31.808
    NFYC Divided nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Measured 3620.77 4763.34 1.31556
    137 CACNG2 Subtracted voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Rooted 49.2925 62.397 13.1045
    CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Measured 12786.6 10879.9 1906.7
    CDK3 Divided cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Squared 81606.8 56215.8 1.45167
    FOXP3 Subtracted forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Ranked 263.191 231.394 31.797
    MSI2 Divided musashi 2 isoform a. [refseq;acc:nm_138962] Rooted 54.9787 66.2416 1.20486
    NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Measured 3620.77 4763.34 1.31556
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Ranked 350 290 1.2069
    SGTA Subtracted small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Squared 69549 92953.5 23404.5
    138 CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Rooted 49.293 62.3973 13.1043
    HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Squared 70739 93908.8 23169.8
    KCNIP1 Divided kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Measured 2755.15 2094.3 1.31555
    MSI1 musashi 1. [refseq;acc:nm_002442] Rooted 54.9787 66.2416 1.20486
    PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Ranked 194.372 234.204 1.20493
    TIPRL Subtracted cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 174.667 205.556 30.889
    TP53BP2 tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Measured 15182.5 13277.9 1904.6
    UBAC1 Divided putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Squared 468498 322755 1.45156
    139 APBA1 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] Ranked 271.752 225.68 1.20415
    CACNG5 Subtracted voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Rooted 49.3267 62.4167 13.09
    CCNB2 Divided g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Squared 81592.1 56211.1 1.45153
    CDC2 Subtracted cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Measured 12780.7 10876.4 1904.3
    CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Ranked 287.41 256.835 30.575
    KCNIP4 Divided potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Measured 2759.61 2099.49 1.31442
    STAM Subtracted signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Squared 86861.5 65369.7 21491.8

    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/