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 [...,...].
    description Rank Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2401 to 2450 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] 4844 SLMO1 Low confidence 203.909 203.244 1.00327
    erythroid differentiation-related factor 1. [refseq;acc:nm_015608] 3095 C10orf137 High confidence 0.00001 0.00001 1
    3370 Low confidence 200.658 197.607 1.01544
    erythropoietin 4 immediate early response; uncharacterized hypothalamus protein ht010. [refseq;acc:nm_018471] 2583 ZC3H15 202.361 198.784 1.01799
    espin. [refseq;acc:nm_031475] 1257 ESPNP High confidence 219.354 224.7 1.02437
    2885 Low confidence 203.506 200.086 1.01709
    est1p-like protein a. [refseq;acc:nm_017575] 2013 SMG6 202.786 198.919 1.01944
    esterase d (ec 3.1.1.1). [swissprot;acc:p10768] 1345 ESD 200.431 196.093 1.02212
    2429 High confidence 192.871 193.555 1.00355
    estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] 1050 HSD17B1 211.449 217.998 1.03097
    1802 Low confidence 199.594 195.657 1.02012
    estradiol 17 beta-dehydrogenase 3 (ec 1.1.1.62) (17-beta-hsd 3) (testicular 17-beta-hydroxysteroid dehydrogenase). [swissprot;acc:p37058] 2232 HSD17B3 203.387 199.611 1.01892
    estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659] 1768 HSD17B4 High confidence 185.276 187.534 1.01219
    3638 Low confidence 190.94 188.276 1.01415
    estradiol 17 beta-dehydrogenase 7 (ec 1.1.1.62) (17-beta-hsd 7) (17- beta-hydroxysteroid dehydrogenase 7). [swissprot;acc:p56937] 2136 HSD17B7 196.594 192.899 1.01916
    estrogen sulfotransferase (ec 2.8.2.4) (sulfotransferase, estrogen- preferring) (est-1). [swissprot;acc:p49888] 1937 SULT1E1 206.037 202.058 1.01969
    estrogen-related receptor beta like 1; huntingtin interacting protein-1 interacting protein; hip1 protein interactor. [refseq;acc:nm_018010] 2862 IFT57 200.418 197.043 1.01713
    estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 1042 no value High confidence 186.799 181.127 1.03132
    2785 Low confidence 200.981 197.544 1.0174
    ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6] 2378 ETNK1 High confidence 212.724 213.574 1.004
    2698 Low confidence 200.085 196.633 1.01756
    ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9] 2377 ETNK2 High confidence 212.724 213.574 1.004
    2565 Low confidence 199.947 196.409 1.01801
    ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] 1758 PCYT2 High confidence 233.45 230.595 1.01238
    2753 Low confidence 201.614 198.157 1.01745
    eukaryotic initiation factor 4a-i (eif-4a-i) (eif4a-i). [swissprot;acc:p04765] 1963 SNORA67 201.642 197.768 1.01959
    2868 High confidence 0.00001 0.00001 1
    eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [swissprot;acc:q14240] 2024 EIF4A2 Low confidence 201.699 197.856 1.01942
    2888 High confidence 0.00001 0.00001 1
    eukaryotic initiation factor 4a-like nuk-34. [swissprot;acc:p38919] 1965 EIF4A3 Low confidence 201.491 197.62 1.01959
    eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] 772 ETF1 High confidence 210.946 221.225 1.04873
    891 Low confidence 203.493 198.443 1.02545
    eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] 1341 EIF2S1 High confidence 226.433 231.491 1.02234
    3096 Low confidence 200.371 197.118 1.0165
    eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] 1839 EIF2S2 High confidence 221.525 224.001 1.01118
    2717 Low confidence 200.642 197.188 1.01752
    eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] 1865 EIF2S3 High confidence 221.639 224.046 1.01086
    3158 Low confidence 201.413 198.197 1.01623
    eukaryotic translation initiation factor 3 subunit 1 (eif-3 alpha) (eif3 p35) (eif3j). [swissprot;acc:o75822] 4681 EIF3J 194.304 193.169 1.00588
    eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] 904 EIF3A High confidence 246.354 237.223 1.03849
    2223 Low confidence 202.056 198.298 1.01895
    eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] 1565 EIF3K High confidence 221.128 224.767 1.01646
    1998 Low confidence 205.081 201.165 1.01947
    eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 746 EIF3I High confidence 250.465 238.38 1.0507
    3357 Low confidence 199.38 196.331 1.01553
    eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] 903 EIF3G High confidence 246.354 237.223 1.03849
    2018 Low confidence 199.773 195.965 1.01943
    eukaryotic translation initiation factor 3 subunit 5 (eif-3 epsilon) (eif3 p47 subunit) (eif3f). [swissprot;acc:o00303] 3260 EIF3F 200.796 197.679 1.01577
    eukaryotic translation initiation factor 3 subunit 6 (eif-3 p48) (eif3e) (mammary tumor-associated protein int-6) (viral integration site protein int-6). [swissprot;acc:q64252] 874 EIF3E 203.141 198.068 1.02561
    eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262] 1454 EIF3EIP 204.525 200.2 1.0216

    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/