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 Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 1963 to 2012 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    246 Ranked eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] High confidence EIF4G3 1.11748 237.312 212.363
    homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Low confidence HOXA5 1.04682 162.755 155.476
    Squared glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence PYGB 1.31131 8875.01 6768.05
    solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] Low confidence SLC2A6 1.09335 51235.5 46861.2
    Rooted jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] JAG2 1.05708 66.0188 69.7871
    myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] High confidence no value 1.13683 146.94 167.046
    247 Measured cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] Low confidence TP53 1.0631 8509.51 9046.45
    wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] High confidence WAS 1.22574 6416.68 7865.15
    Ranked homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence no value 1.04682 162.755 155.476
    rna-binding protein. [refseq;acc:nm_019027] High confidence 1.11719 237.302 212.41
    Squared glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] PYGL 1.31131 8875.01 6768.05
    solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64] Low confidence SLC2A8 1.09335 51235.5 46861.2
    Rooted myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] MEF2D 1.05708 66.0196 69.7878
    probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] High confidence DDX56 1.13668 47.3621 53.8355
    248 Measured proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] CRK 1.22477 6417.18 7859.6
    rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Low confidence RABEP1 1.06302 7615.71 8095.68
    Ranked apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] High confidence no value 1.11719 237.302 212.41
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Low confidence HSD17B14 1.04682 162.755 155.476
    Squared myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] High confidence MYO15A 1.31131 8875.01 6768.05
    programmed cell death 4 isoform 1; programmed cell death 4; nuclear antigen h731. [refseq;acc:nm_014456] Low confidence PDCD4 1.09312 50352.9 46063.3
    Rooted jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] JAG1 1.05708 66.0195 69.7877
    u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] High confidence LSM5 1.13264 56.0466 63.4808
    249 Measured apg3p; pc3-96 protein. [refseq;acc:nm_022488] Low confidence ATG3 1.06276 10547.4 9924.56
    tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] High confidence ABL2 1.22477 6417.18 7859.59
    Ranked dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] Low confidence DUOX1 1.0468 210.487 201.076
    ns1-associated protein 1. [refseq;acc:nm_006372] High confidence SYNCRIP 1.11719 237.302 212.41
    Squared glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] PYGM 1.31131 8875.01 6768.05
    ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Low confidence RGL1 1.09241 49409.1 45229.3
    Rooted myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] MEF2C 1.05708 66.0195 69.7877
    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] High confidence BRF1 1.13199 55.5965 62.9349
    250 Measured large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] Low confidence SLC7A8 1.06261 6975.98 7412.76
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] High confidence no value 1.22477 6417.18 7859.6
    Ranked diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Low confidence DGAT1 1.04671 210.443 201.051
    heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] High confidence HNRNPR 1.11719 237.302 212.41
    Squared c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] CTBP2 1.30536 69201.8 53013.4
    rab11-family interacting protein 4. [refseq;acc:nm_032932] Low confidence RAB11FIP4 1.09213 34469.6 37645.4
    Rooted myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] MEF2A 1.05708 66.0188 69.7871
    nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] High confidence NOLA1 1.13199 55.5965 62.9349
    251 Measured kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Low confidence KYNU 1.06221 8527.55 9058.09
    tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] High confidence HCK 1.22477 6417.18 7859.6
    Ranked nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] Low confidence NOX5 1.04666 210.415 201.035
    oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] High confidence SLC15A1 1.11707 186.172 166.661
    Squared b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] BCL6B 1.30521 69165.6 52992.1
    eferin. [swissprot;acc:o75154] Low confidence RAB11FIP3 1.09213 34469.6 37645.4
    Rooted max protein. [swissprot;acc:p25912] High confidence MAX 1.13159 56.3054 63.7148
    septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Low confidence SEPT7 1.05707 90.452 95.6145
    252 Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] AGPAT3 1.06194 8492.92 9018.94
    crk-like protein. [swissprot;acc:p46109] High confidence CRKL 1.22477 6417.18 7859.6
    Ranked cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839] Low confidence CYBB 1.04665 210.414 201.035
    eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] High confidence EIF4G1 1.11689 237.292 212.457

    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/