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 description Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1712 to 1761 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    214 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] CACNG5 Divided Measured 4074.83 5086.49 1.24827
    215 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] STAMBP Rooted 105.205 92.2415 1.14054
    eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 Subtracted Ranked 237.292 212.457 24.835
    homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 Rooted 121.695 131.815 10.12
    myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] no value Divided Ranked 112 126 1.125
    plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] CPB2 Subtracted Measured 7711.31 6265.76 1445.55
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] CHMP4A Squared 28994.2 17134.8 11859.4
    protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] PRKCH Divided 86609.4 65234.5 1.32766
    transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] KRAS Measured 16074 12888.4 1.24717
    216 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] ECHS1 Subtracted 10067.9 11511 1443.1
    homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] no value Rooted 121.695 131.815 10.12
    j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] RBPJ Squared 46785.7 58383.2 11597.5
    leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] SHOC2 Divided Measured 16071.6 12886.8 1.24714
    myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] MYH4 Ranked 112 126 1.125
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] VPS24 Rooted 105.205 92.2415 1.14054
    protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] PRKCE Squared 86600.9 65229.9 1.32763
    small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] SNRPD2 Subtracted Ranked 226.471 201.769 24.702
    217 60s ribosomal protein l26. [swissprot;acc:q02877] RPL26 242.326 267.008 24.682
    human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] HIVEP3 Squared 46785.7 58383.2 11597.5
    myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] MYH8 Divided Ranked 112 126 1.125
    peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] PPIB Squared 86600.9 65229.9 1.32763
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] CHMP4A Rooted 105.205 92.2415 1.14054
    proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] CRK Subtracted Measured 6417.18 7859.6 1442.42
    ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] no value Divided 16071.6 12886.8 1.24714
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 Subtracted Rooted 121.695 131.815 10.12
    218 60s ribosomal protein l35. [swissprot;acc:p42766] RPL35 Ranked 242.333 266.999 24.666
    hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] no value Divided Rooted 46.1476 52.5742 1.13926
    myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] MYH2 Ranked 112 126 1.125
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] no value Subtracted Measured 6417.18 7859.6 1442.42
    t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] CCT3 Rooted 107.178 117.276 10.098
    transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] HRAS Divided Measured 16070.4 12886 1.24712
    udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] OGT Squared 86600.9 65229.9 1.32763
    zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] HIVEP1 Subtracted 46785.7 58383.2 11597.5
    219 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] no value Ranked 242.339 266.986 24.647
    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] COX4I1 Divided Squared 86600.9 65229.9 1.32763
    histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] HAT1 Subtracted Rooted 44.963 55.0576 10.0946
    histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] RBBP7 Divided 52.7146 60.0088 1.13837
    human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] HIVEP2 Subtracted Squared 46785.7 58383.2 11597.5
    myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] MYH3 Divided Ranked 112 126 1.125
    transforming protein n-ras. [swissprot;acc:p01111] no value Measured 16069.8 12885.6 1.24711
    tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] HCK Subtracted 6417.18 7859.6 1442.42
    220 brain protein 44. [swissprot;acc:o95563] BRP44 Rooted 113.374 123.463 10.089
    crk-like protein. [swissprot;acc:p46109] CRKL Measured 6417.18 7859.6 1442.42
    cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] COX4I2 Divided Squared 86600.9 65229.9 1.32763
    mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] no value Measured 41482.5 33356.5 1.24361
    metastasis-associated protein mta1. [swissprot;acc:q13330] MTA1 Rooted 52.7557 60.035 1.13798
    mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] MRPL2 Subtracted Ranked 242.339 266.986 24.647
    myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] MYH1 Divided 112 126 1.125
    transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] TAF7 Subtracted Squared 57808.9 46630.3 11178.6
    221 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] PSCD1 Divided Measured 41482.5 33356.5 1.24361

    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/