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.


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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 description Value Type 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
description
Value Type
red
green
network_comparison
1398 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] Measured 5803.12 6256.05 1.07805
nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838] Squared 50588.2 45100.2 1.12168
1399 calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] Rooted 62.3815 64.865 1.03981
eyes absent homolog 2. [swissprot;acc:o00167] Ranked 218.417 213.848 1.02137
heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795] Measured 5803.1 6256.03 1.07805
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] Squared 50587.2 45099.6 1.12168
1400 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] Ranked 218.667 214.118 1.02125
heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] Measured 5803.45 6256.43 1.07805
nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653] Squared 50587.8 45099.9 1.12168
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Rooted 62.3815 64.865 1.03981
1401 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] Ranked 218.657 214.11 1.02124
hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] Measured 5728.92 6175.99 1.07804
rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799] Rooted 62.3815 64.865 1.03981
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] Squared 25427.4 28520.7 1.12165
1402 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] Measured 6160.06 6640.78 1.07804
colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] Ranked 209.682 205.329 1.0212
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] Rooted 66.6073 69.2586 1.0398
udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] Squared 25427.4 28520.7 1.12165
1403 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] Rooted 68.5259 71.2383 1.03958
enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Ranked 184.656 180.823 1.0212
importin 4. [refseq;acc:nm_024658] Measured 5613.16 6050.16 1.07785
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] Squared 23178.4 25996.4 1.12158
1404 mesoderm induction early response 1. [refseq;acc:nm_020948] Measured 6291.89 6781.6 1.07783
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Rooted 100.26 96.4491 1.03951
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] Squared 19596.8 21975 1.12136
splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] Ranked 232.752 237.65 1.02104
1405 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] Squared 19596.4 21974.6 1.12136
eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] Ranked 245.532 240.483 1.021
proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] Measured 6291.89 6781.6 1.07783
ubiquitin. [swissprot;acc:p02248] Rooted 68.5562 71.2644 1.0395
1406 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
dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] Squared 24597.4 27579 1.12122
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Ranked 212.833 208.456 1.021
ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477] Measured 6210.51 6693.49 1.07777
1407 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] Rooted 61.0274 63.4251 1.03929
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Squared 29964.5 33596.3 1.1212
transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] Measured 5692.53 6134.64 1.07766
wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830] Ranked 206.104 210.424 1.02096
1408 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] Squared 29964.5 33596.3 1.1212
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] Rooted 61.0274 63.4251 1.03929
serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] Measured 6268.94 6755.57 1.07763
stromal interaction molecule 1 precursor. [swissprot;acc:q13586] Ranked 206.102 210.42 1.02095
1409 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] Squared 21512.7 24115.7 1.121
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] Measured 5358.19 5773.37 1.07749
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Rooted 65.3456 67.9119 1.03927
trap/mediator complex component trap25. [refseq;acc:nm_080651] Ranked 206.102 210.42 1.02095
1410 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] Measured 6274.62 6760.78 1.07748
heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] Rooted 65.3456 67.9119 1.03927
malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Squared 17102.5 19171.7 1.12099
wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] Ranked 206.1 210.417 1.02095

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/