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.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5591 to 5640 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
1398 Squared nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838] 50588.2 45100.2 1.12168
Rooted calmegin precursor. [swissprot;acc:o14967] 62.3815 64.865 1.03981
1399 Measured heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795] 5803.1 6256.03 1.07805
Ranked eyes absent homolog 2. [swissprot;acc:o00167] 218.417 213.848 1.02137
Squared nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653] 50587.2 45099.6 1.12168
Rooted calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] 62.3815 64.865 1.03981
1400 Measured heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] 5803.45 6256.43 1.07805
Ranked cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] 218.667 214.118 1.02125
Squared nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653] 50587.8 45099.9 1.12168
Rooted soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] 62.3815 64.865 1.03981
1401 Measured hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] 5728.92 6175.99 1.07804
Ranked cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] 218.657 214.11 1.02124
Squared ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [swissprot;acc:q93068] 25427.4 28520.7 1.12165
Rooted rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799] 62.3815 64.865 1.03981
1402 Measured 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 6160.06 6640.78 1.07804
Ranked colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] 209.682 205.329 1.0212
Squared udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] 25427.4 28520.7 1.12165
Rooted cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] 66.6073 69.2586 1.0398
1403 Measured importin 4. [refseq;acc:nm_024658] 5613.16 6050.16 1.07785
Ranked enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 184.656 180.823 1.0212
Squared serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] 23178.4 25996.4 1.12158
Rooted alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 68.5259 71.2383 1.03958
1404 Measured mesoderm induction early response 1. [refseq;acc:nm_020948] 6291.89 6781.6 1.07783
Ranked splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] 232.752 237.65 1.02104
Squared ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] 19596.8 21975 1.12136
Rooted protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 100.26 96.4491 1.03951
1405 Measured proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] 6291.89 6781.6 1.07783
Ranked eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 245.532 240.483 1.021
Squared 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 19596.4 21974.6 1.12136
Rooted ubiquitin. [swissprot;acc:p02248] 68.5562 71.2644 1.0395
1406 Measured ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477] 6210.51 6693.49 1.07777
Ranked orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] 212.833 208.456 1.021
Squared dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 24597.4 27579 1.12122
Rooted cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] 61.6284 64.0609 1.03947
1407 Measured transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] 5692.53 6134.64 1.07766
Ranked wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830] 206.104 210.424 1.02096
Squared preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] 29964.5 33596.3 1.1212
Rooted lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] 61.0274 63.4251 1.03929
1408 Measured serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] 6268.94 6755.57 1.07763
Ranked stromal interaction molecule 1 precursor. [swissprot;acc:q13586] 206.102 210.42 1.02095
Squared dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] 29964.5 33596.3 1.1212
Rooted lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055] 61.0274 63.4251 1.03929
1409 Measured glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808] 5358.19 5773.37 1.07749
Ranked trap/mediator complex component trap25. [refseq;acc:nm_080651] 206.102 210.42 1.02095
Squared 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] 21512.7 24115.7 1.121
Rooted peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] 65.3456 67.9119 1.03927
1410 Measured delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] 6274.62 6760.78 1.07748
Ranked wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] 206.1 210.417 1.02095
Squared malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] 17102.5 19171.7 1.12099
Rooted heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] 65.3456 67.9119 1.03927

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
- 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/