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 description Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 3101 to 3150 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    388 IRX2 iroquois-class homeodomain protein irx-2 (iroquois homeobox protein 2) (fragment). [swissprot;acc:q9bzi1] Measured Low confidence 8966.8 9445.26 1.05336
    SLC16A1 monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985] Rooted 82.9808 86.9781 1.04817
    SRR serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] High confidence 50.3345 45.6718 1.10209
    SYVN1 hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431] Squared Low confidence 48960.5 45772 1.06966
    389 CCRN4L nocturnin (ccr4 protein homolog). [swissprot;acc:q9uk39] Rooted 69.1568 72.4882 1.04817
    CUTL2 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Measured 8159.97 8595.12 1.05333
    DDX6 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] High confidence 4533.74 5279.4 1.16447
    HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Ranked Low confidence 200.049 192.942 1.03683
    RACGAP1 rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] Squared 45959.5 42968.2 1.06962
    RARS2 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] High confidence 31819.7 39222.2 1.23264
    RPL34 60s ribosomal protein l34. [swissprot;acc:p49207] Rooted 50.3345 45.6718 1.10209
    SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Ranked 227.575 208.756 1.09015
    390 no value nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Squared 28895.6 35572.8 1.23108
    solute carrier family 35, member e2. [refseq;acc:nm_182838] Ranked Low confidence 203.647 211.144 1.03681
    HS6ST1 heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] Squared 47629.9 44535.1 1.06949
    MRPL13 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Ranked High confidence 241.828 263.62 1.09011
    SEC61A2 protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Rooted 50.3345 45.6718 1.10209
    SLC16A7 monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] Low confidence 82.9732 86.9699 1.04817
    TLR2 toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Measured 6983.51 7354.87 1.05318
    TMEM131 rw1 protein (fragment). [swissprot;acc:q92545] High confidence 4533.74 5279.4 1.16447
    391 ATP6V0A1 vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Low confidence 8552.2 9004.53 1.05289
    HTRA2 serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Ranked 200.046 192.943 1.03681
    KPNB1 importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Squared High confidence 28895.6 35572.8 1.23108
    PRODH2 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Low confidence 50781.5 47483.2 1.06946
    RPS16 40s ribosomal protein s16. [swissprot;acc:p17008] Ranked High confidence 241.828 263.62 1.09011
    SEC61A1 protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Rooted 50.3345 45.6718 1.10209
    SLC16A8 monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907] Low confidence 82.9474 86.9421 1.04816
    TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Measured High confidence 3658.76 3144.39 1.16358
    392 DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 3641.89 4236.95 1.16339
    LIMD1 lim domains containing 1. [refseq;acc:nm_014240] Rooted Low confidence 70.7384 74.1429 1.04813
    NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Ranked 200.894 193.766 1.03679
    RPL13A 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] High confidence 241.83 263.615 1.09008
    RPL3L 60s ribosomal protein l3-like. [swissprot;acc:q92901] Rooted 50.3313 45.6913 1.10155
    RRS1 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Squared Low confidence 49539.3 46326.1 1.06936
    SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Measured 7781.34 8192.41 1.05283
    TBL1X transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Squared High confidence 28895.6 35572.8 1.23108
    393 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Ranked Low confidence 201.334 194.242 1.03651
    AK2 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] Squared 47766.3 44669.1 1.06934
    CRY1 cryptochrome 1 (photolyase-like). [refseq;acc:nm_004075] Measured 8673.83 9132.05 1.05283
    EIF4E eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] High confidence 4490.28 5222.25 1.16301
    POLR2A dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Rooted 49.8842 45.2875 1.1015
    SLC16A3 monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] Low confidence 82.865 86.8534 1.04813
    TBL1Y transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Squared High confidence 28895.6 35572.8 1.23108
    TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Ranked 225.719 207.072 1.09005
    394 no value probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1] Rooted Low confidence 70.7384 74.1429 1.04813
    BAIAP3 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Measured High confidence 4490.28 5222.25 1.16301
    CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Rooted 58.6533 64.5958 1.10132
    CLP1 pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Squared Low confidence 48577.7 45429.7 1.06929
    CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Ranked 204.815 197.606 1.03648
    DPP9 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] High confidence 218.827 238.407 1.08948

    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/