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 Filtered Interaction Map red green network_comparison
    Results: HTML CSV LaTeX Showing element 2680 to 2729 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    1340 TBC1D5 tbc1 domain family member 5. [swissprot;acc:q92609] Low confidence 203.872 199.458 1.02213
    1341 EIF2S1 eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] High confidence 226.433 231.491 1.02234
    RECK reversion-inducing cysteine-rich protein with kazal motifs precursor (hreck) (suppressor of tumorigenicity 15) (st15). [swissprot;acc:o95980] Low confidence 187.632 183.57 1.02213
    1342 CHPT1 choline phosphotransferase 1; cholinephosphotransferase 1 alpha; cholinephosphotransferase 1. [refseq;acc:nm_020244] 187.631 183.569
    SUV39H1 histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463] High confidence 226.433 231.491 1.02234
    1343 CDC25A m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] 258.558 252.916 1.02231
    MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Low confidence 153.029 156.416 1.02213
    1344 CSNK2A2 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 204.058 199.639
    EXO1 exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] High confidence 216.772 221.594 1.02224
    1345 ESD esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Low confidence 200.431 196.093 1.02212
    FANCL phd finger protein 9. [refseq;acc:nm_018062] High confidence 216.772 221.594 1.02224
    1346 SOLH small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632]
    VPS35 vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Low confidence 201.165 196.812 1.02212
    1347 LIAS lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] High confidence 204.961 209.517 1.02223
    MRPL24 mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] Low confidence 205.323 200.881 1.02211
    1348 PPIF peptidyl-prolyl cis-trans isomerase, mitochondrial precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin f). [swissprot;acc:p30405] 201.458 197.1
    ZIC1 zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] High confidence 218.569 213.832 1.02215
    1349 CPA5 carboxypeptidase a5. [refseq;acc:nm_080385] Low confidence 187.671 183.613 1.0221
    ZIC3 zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] High confidence 218.572 213.841 1.02212
    1350 CCT8 t-complex protein 1, theta subunit (tcp-1-theta) (cct-theta). [swissprot;acc:p50990] Low confidence 201.762 197.399 1.0221
    ZIC2 zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] High confidence 218.574 213.847
    1351 NUCB2 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Low confidence 211.431 216.104
    PHB prohibitin. [swissprot;acc:p35232] High confidence 211.513 206.941 1.02209
    1352 no value repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]
    CPB1 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Low confidence 187.651 183.595
    1353 FRK tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 201.009 196.664
    NDST2 heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] High confidence 228.409 223.475 1.02208
    1354 NDST3 n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784]
    UBQLN1 ubiquilin 1 isoform 1. [refseq;acc:nm_013438] Low confidence 206.622 202.158
    1355 NDST4 n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] High confidence 228.409 223.475
    RASA3 ras gtpase-activating protein 3 (gap1(ip4bp)) (ins p4-binding protein). [swissprot;acc:q14644] Low confidence 202.643 198.269 1.02206
    1356 no value ca2+-promoted ras inactivator; gtpase activating protein-like; calcium-promoted ras inactivator. [refseq;acc:nm_006989]
    NDST1 heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848] High confidence 228.409 223.475 1.02208
    1357 CDC27 protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260]
    RASA2 ras gtpase-activating protein 2 (gap1m). [swissprot;acc:q15283] Low confidence 202.643 198.269 1.02206
    1358 RASAL1 rasgap-activating-like protein 1. [swissprot;acc:o95294]
    USF1 upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] High confidence 214.987 210.359 1.022
    1359 GSTT2B glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 228.642 223.726 1.02197
    RASA4 rasgap-activating-like protein 2. [swissprot;acc:o43374] Low confidence 202.643 198.269 1.02206
    1360 PPIE peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] 201.201 196.865 1.02203
    TGFBR1 tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] High confidence 223.89 228.805 1.02195
    1361 SFRS10 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] Low confidence 203.394 199.014 1.02201
    USF2 upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] High confidence 214.971 210.354 1.02195
    1362 PAOX peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] 228.644 223.736 1.02194
    RCAN1 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] Low confidence 203.714 199.329 1.022
    1363 CREB5 camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] High confidence 218.591 213.899 1.02194
    F11R junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624] Low confidence 200.065 195.758 1.022
    1364 ACVR1B serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] High confidence 223.885 228.797 1.02194
    LMLN leishmanolysin-like (metallopeptidase m8 family); leishmanolysin-2. [refseq;acc:nm_033029] Low confidence 208.235 203.754 1.02199
    1365 ATPIF1 atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] High confidence 228.644 223.736 1.02194

    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/