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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1858 to 1907 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    929 MPDU1 mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] High confidence 225.955 1.03642 218.015
    930 C19orf56 protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] Low confidence 205.137 1.02503 200.128
    PKM2 pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] High confidence 231.357 1.0364 239.778
    931 BHLHB4 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 159.13 1.03637 164.917
    ETV7 transcription factor tel-2 (ets-related protein tel2) (tel related ets factor). [swissprot;acc:q9y603] Low confidence 205.137 1.02503 200.128
    932 FBP1 fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 190.502 1.02502 185.852
    MTRF1L mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] High confidence 225.939 1.03636 218.013
    933 BHLHB5 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] 159.165 1.03635 164.951
    SEL1L2 dj842g6.2 (novel protein imilar to sel1l (sel-1 (suppressor of lin-12, c.elegans)-like)) (fragment). [sptrembl;acc:q9ugd3] Low confidence 190.447 1.025 185.802
    934 NOL6 nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] High confidence 242.024 1.03631 233.544
    SEL1L sel-1 homolog precursor (suppressor of lin-12-like protein) (sel-1l). [swissprot;acc:q9ubv2] Low confidence 190.447 1.02499 185.803
    935 no value sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] High confidence 232.473 1.03611 224.372
    ICT1 immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] Low confidence 200.801 1.02498 195.908
    936 no value casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] High confidence 232.473 1.03611 224.372
    FBP2 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Low confidence 190.386 1.02497 185.747
    937 no value spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 194.236 189.504
    SF3A3 splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] High confidence 220.246 1.03588 212.618
    938 SF3A1 splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]
    SNAP91 clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Low confidence 203.609 1.02497 198.648
    939 BRCA1 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] High confidence 216.501 1.03588 224.27
    SGCD delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Low confidence 206.817 1.02496 201.78
    940 CAPNS1 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] High confidence 212.442 1.03586 205.088
    VPS29 vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Low confidence 202.747 1.02496 197.81
    941 ARID1A swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] High confidence 212.437 1.03586 205.083
    HACL1 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] Low confidence 207.026 1.02493 201.99
    942 GCA grancalcin. [swissprot;acc:p28676] High confidence 212.442 1.03586 205.088
    LIN7C lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] Low confidence 207.862 1.02492 202.809
    943 NDUFB5 nadh-ubiquinone oxidoreductase sgdh subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-sgdh) (ci-sgdh). [swissprot;acc:o43674] 205.602 200.603
    SRI sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] High confidence 212.442 1.03586 205.087
    944 GHITM growth hormone inducible transmembrane protein (dermal papilla derived protein 2) (my021 protein) (ptd010). [swissprot;acc:q9h3k2] Low confidence 204.752 1.02491 199.775
    PDCD6 programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] High confidence 212.437 1.03586 205.083
    945 ARID1B brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 212.44 205.085
    ZNF547 sedlin. [swissprot;acc:o14582] Low confidence 195.693 1.02491 190.937
    946 no value histone h4. [swissprot;acc:p02304] High confidence 227.765 1.03576 219.902
    VPS45 vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Low confidence 204.752 1.02491 199.775
    947 NOC3L ad24 protein. [refseq;acc:nm_022451] 203.472 1.02488 198.533
    SORBS2 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] High confidence 212.51 1.03567 205.191
    948 PBK t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Low confidence 209.239 1.02485 204.165
    TOM1 target of myb protein 1. [swissprot;acc:o60784] High confidence 217.254 1.03541 209.824
    949 no value huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] 217.253 1.0354 209.826
    SRD5A1 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] Low confidence 204.147 1.02485 199.196
    950 ERCC5 dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] High confidence 252.873 1.03539 261.821
    SRD5A2 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] Low confidence 204.147 1.02485 199.196
    951 DTNBP1 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] 203.779 1.02483 198.841
    TRIO triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] High confidence 217.253 1.03539 209.827
    952 ATP6V0A2 vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Low confidence 190.738 1.02482 186.118
    TOM1L2 target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] High confidence 217.252 1.03537 209.83
    953 no value heat shock factor binding protein 1. [swissprot;acc:o75506] Low confidence 206.826 1.02481 201.818
    EXOSC10 polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] High confidence 198.494 1.03512 205.466
    954 GSTZ1 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] 267.447 1.03487 276.773

    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/