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 Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 5908 to 5957 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
green
red
network_comparison
739 phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] Divided Ranked 235.027 223.58 1.0512
ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] Squared 30046.7 25727.7 1.16787
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Subtracted Rooted 64.9858 60.6572 4.3286
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Squared 30514.1 26312 4202.1
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Measured 5901.72 5248.07 653.65
740 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] Divided Ranked 235.027 223.58 1.0512
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Rooted 56.7251 53.1114 1.06804
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Squared 25775.1 22075.1 1.16761
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Subtracted Rooted 90.7685 95.094 4.3255
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Squared 16522.9 12326.4 4196.5
syntaxin 7. [swissprot;acc:o15400] Measured 6233.52 5580.97 652.55
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Ranked 212.875 223.463 10.588
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Divided Measured 6434.78 5768.32 1.11554
741 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Rooted 56.7251 53.1114 1.06804
dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Subtracted 69.648 65.3248 4.3232
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Divided Measured 6434.78 5768.32 1.11554
multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Ranked 235.027 223.58 1.0512
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Squared 27894.5 23894.7 1.16739
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Subtracted 16522.9 12326.4 4196.5
sipl protein. [refseq;acc:nm_018269] Measured 7175.18 6522.94 652.24
step ii splicing factor slu7. [refseq;acc:nm_006425] Ranked 212.875 223.463 10.588
742 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Measured 5514.87 4864.66 650.21
brain protein 44. [swissprot;acc:o95563] Divided Ranked 120.078 126.215 1.05111
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Subtracted Squared 16522.9 12326.4 4196.5
eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Divided Measured 4607.9 4131.04 1.11543
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Subtracted Ranked 215.541 226.003 10.462
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Divided Squared 36662.8 31406.6 1.16736
syntaxin 12. [refseq;acc:nm_177424] Subtracted Rooted 65.66 61.3557 4.3043
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Divided 71.5506 67.0234 1.06755
743 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Subtracted Measured 5514.87 4864.66 650.21
cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Divided Squared 36662.8 31406.6 1.16736
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Measured 4607.9 4131.04 1.11543
katanin p60 subunit a 1. [refseq;acc:nm_007044] Rooted 51.0573 54.4988 1.0674
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Subtracted Ranked 215.535 225.996 10.461
nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000] Squared 36239.4 32053.5 4185.9
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Divided Ranked 120.078 126.215 1.05111
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Subtracted Rooted 46.0753 50.3767 4.3014
744 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Divided Squared 36662.8 31406.6 1.16736
c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Subtracted Measured 9253.79 9903.22 649.43
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Divided 11221.1 12515.4 1.11535
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Subtracted Ranked 215.535 225.996 10.461
dynactin 4. [refseq;acc:nm_032486] Divided Rooted 51.7372 55.2242 1.0674
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Subtracted 65.306 61.0082 4.2978
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Squared 35762.8 31586.9 4175.9
septin 6. [swissprot;acc:q14141] Divided Ranked 120.463 126.604 1.05098
745 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Subtracted Measured 9251.2 9899.79 648.59
cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Divided Squared 36662.8 31406.6 1.16736
histone deacetylase 1 (hd1). [swissprot;acc:q13547] Subtracted Ranked 215.53 225.989 10.459
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Squared 31257.9 27084.5 4173.4
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Rooted 65.3071 61.0097 4.2974

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/