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 199 to 248 of 502 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 0
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    199 no value 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 11781.8 10545.7 1.11721
    200 MTRF1 peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 8786.74 7870.3 1.11644
    201 no value maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 16853 15123 1.1144
    202 serpin b11. [swissprot;acc:q96p15]
    203 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
    204 DPP8 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 15081.8 16802.1 1.11406
    205 no value 60s ribosomal protein l23a. [swissprot;acc:p29316] 11844.9 10636.3 1.11363
    206 hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] 7479 6716 1.11361
    207 dc11 protein. [refseq;acc:nm_020186]
    208 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 11846.3 10638.4 1.11354
    209 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 775 696 1.11351
    210 MMS19 mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 17144.8 15405.6 1.11289
    211 no value ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 10367 9320.25 1.11231
    212 metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] 18241.7 16405 1.11196
    213 P4HB protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] 9379.47 8436.39 1.11179
    214 PET112L probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] 7621.99 8473.85 1.11176
    215 no value myosin vi. [swissprot;acc:q9um54] 10121.5 11250.5 1.11154
    216 GSTZ1 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] 10559.7 11732 1.11102
    217 BIRC5 baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] 7101.79 6406.18 1.10858
    218 no value lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 19355 17469.2 1.10795
    219 SDHA succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] 12196.2 11009.7 1.10777
    220 NCALD neurocalcin delta. [swissprot;acc:p29554] 13973.6 15473.5 1.10734
    221 no value estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 12190.3 13497.2 1.10721
    222 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 12183 11013.2 1.10622
    223 pnas-18. [sptrembl;acc:q9bzu3] 12602.7 13939.6 1.10608
    224 CLPX atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 9815.6 8889.93 1.10413
    225 no value 40s ribosomal protein s29. [swissprot;acc:p30054] 11035.3 9997.71 1.10378
    226 rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] 15395.7 16992.9 1.10374
    227 TIGD6 tigger transposable element derived 6. [refseq;acc:nm_030953] 12360 11200.2 1.10355
    228 SEPSECS soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] 10303.5 11370.4
    229 no value poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 10899.4 9878.1 1.10339
    230 TIGD7 tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] 12364.7 11207.7 1.10323
    231 TIGD1 tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] 12364.8 11207.9 1.10322
    232 KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 12394.7 11240.2 1.10271
    233 no value 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 9586.97 10560 1.1015
    234 transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] 16614 18296 1.10124
    235 EEF1AL3 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] 14554.5 16027.9 1.10123
    236 PPP1R2 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 15245.4 16788.5 1.10122
    237 no value bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 9984 9067 1.10114
    238 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 12677.7 13941.7 1.0997
    239 MTO1 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] 8907.41 9795.36 1.09969
    240 no value methyltransferase like 2. [refseq;acc:nm_018396] 17946 16326 1.09923
    241 secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] 14003.7 12743.3 1.09891
    242 GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 15260.6 13895.8 1.09822
    243 PABPC3 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 1251 1373 1.09752
    244 KRTAP9-8 keratin associated protein 9.2. [refseq;acc:nm_031961] 10551.1 11579.9 1.09751
    245 CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 11867.6 13019 1.09702
    246 no value keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 10551.6 11573.7 1.09687
    247 keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]
    248 keratin associated protein 1.5. [refseq;acc:nm_031957]

    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/