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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Gene description measured Rank final expected Hugo
Results: HTML CSV LaTeX Showing element 2708 to 2757 of 3206 in total
description
measured
Rank
final
expected
Hugo
SERINE/THREONINE-PROTEIN KINASE PAK 3 (EC 2.7.1.-) (P21-ACTIVATED KINASE 3) (PAK-3) (BETA-PAK) (OLIGOPHRENIN-3). [SWISSPROT;Acc:O75914] 0.048732 2183 0.226549825 0.215105 PAK3
SERINE/THREONINE-PROTEIN KINASE PAK 4 (EC 2.7.1.-) (P21-ACTIVATED KINASE 4) (PAK-4). [SWISSPROT;Acc:O96013] 0.145818 2795 0.199902118 0.729447 PAK4
SERINE/THREONINE-PROTEIN KINASE PAK 7 (EC 2.7.1.-) (P21-ACTIVATED KINASE 7) (PAK-7) (PAK-5). [SWISSPROT;Acc:Q9P286] 0.193542 2796 0.199902085 0.968184 PAK7
SERINE/THREONINE-PROTEIN KINASE PLK (EC 2.7.1.-) (PLK-1) (SERINE- THREONINE PROTEIN KINASE 13) (STPK13). [SWISSPROT;Acc:P53350] 0.170317 677 0.266025125 0.640229 PLK1
SERINE/THREONINE-PROTEIN KINASE RECEPTOR R2 PRECURSOR (EC 2.7.1.37) (SKR2) (ACTIVIN RECEPTOR-LIKE KINASE 4) (ALK-4) (ACTR-IB). [SWISSPROT;Acc:P36896] 0.150674 1186 0.24866856 0.605923 ACVR1B
SEROLOGICALLY DEFINED COLON CANCER ANTIGEN 16. [RefSeq;Acc:NM_006649] 0.0771492 908 0.258260747 0.298726 UTP14A
SERPIN B11. [SWISSPROT;Acc:Q96P15] 0.0194204 2326 0.221795594 0.0875599 no value
SERPIN B12. [SWISSPROT;Acc:Q96P63] 0.0598165 1577 0.240892506 0.248312 SERPINB12
SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS). [SWISSPROT;Acc:P49591] 0.293395 1848 0.233451626 1.25677 SARS
SESTRIN 1 (P53-REGULATED PROTEIN PA26). [SWISSPROT;Acc:Q9Y6P5] 0.699473 622 0.268259411 2.60745 SESN1
SESTRIN 2 (HI95). [SWISSPROT;Acc:P58004] 0.553815 628 0.268258835 2.06448 SESN2
SESTRIN 3. [SWISSPROT;Acc:P58005] 0.578823 635 0.268258014 2.15771 SESN3
SET DOMAIN AND MARINER TRANSPOSASE FUSION GENE. [RefSeq;Acc:NM_006515] 0.379831 3014 0.121833642 3.11762 SETMAR
SEVEN IN ABSENTIA HOMOLOG 1. [RefSeq;Acc:NM_003031] 0.563143 499 0.274221006 2.05361 no value
SEVEN IN ABSENTIA HOMOLOG 2. [RefSeq;Acc:NM_005067] 0.454535 474 0.274321943 1.65694 SIAH2
SFRS PROTEIN KINASE 1; SR PROTEIN KINASE 1. [RefSeq;Acc:NM_003137] 0.0417611 1340 0.24528272 0.170257 SRPK1
SFRS PROTEIN KINASE 2 ISOFORM B. [RefSeq;Acc:NM_182691] 0.0349958 1338 0.245283336 0.142675 SRPK2
SH2 DOMAIN CONTAINING 3C; NOVEL SH2-CONTAINING PROTEIN 3; SH2 DOMAIN-CONTAINING 3C; LIKELY ORTHOLOG OF MOUSE CAS/HEF1-ASSOCIATED SIGNAL TRANSDUCER. [RefSeq;Acc:NM_005489] 0.122271 187 0.328897676 0.37176 SH2D3C
SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH PROTEIN (SH3BGR PROTEIN) (21- GLUTAMIC ACID-RICH PROTEIN) (21-GARP). [SWISSPROT;Acc:P55822] 0.046789 549 0.271000214 0.172653 SH3BGR
SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN 2 (FOVEA-ASSOCIATED SH3 DOMAIN BINDING PROTEIN). [SWISSPROT;Acc:Q9UJC5] 0.0368814 554 0.270999456 0.136094 no value
SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN. [SWISSPROT;Acc:O75368] 0.0371738 556 0.270999395 0.137173 SH3BGRL
SH3-CONTAINING GRB2-LIKE PROTEIN 1 (SH3 DOMAIN PROTEIN 2B) (EXTRA ELEVEN-NINETEEN LEUKEMIA FUSION GENE) (EEN) (EEN FUSION PARTNER OF MLL). [SWISSPROT;Acc:Q99961] 0.172401 2501 0.215238121 0.800978 SH3GL1
SH3-CONTAINING GRB2-LIKE PROTEIN 2 (SH3 DOMAIN PROTEIN 2A) (ENDOPHILIN 1) (EEN-B1). [SWISSPROT;Acc:Q99962] 0.158519 2497 0.215396343 0.735941 SH3GL2
SH3-CONTAINING GRB2-LIKE PROTEIN 3 (SH3 DOMAIN PROTEIN 2C) (EEN-B2). [SWISSPROT;Acc:Q99963] 0.171407 2493 0.215540136 0.795244 SH3GL3
SHC TRANSFORMING PROTEIN. [SWISSPROT;Acc:P29353] 0.0444669 479 0.274304168 0.162108 SHC1
SHORT COILED-COIL PROTEIN; SHORT COILED COIL PROTEIN. [RefSeq;Acc:NM_032547] 0.0348108 931 0.257461097 0.135208 SCOC
SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 4 (TRPC4) (TRP-RELATED PROTEIN 4) (HTRP-4) (HTRP4). [SWISSPROT;Acc:Q9UBN4] 0.185352 1023 0.253463462 0.731277 TRPC4
SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 5 (TRPC5) (HTRP-5) (HTRP5). [SWISSPROT;Acc:Q9UL62] 0.2166 1026 0.253438859 0.854644 TRPC5
SHROOM-RELATED PROTEIN; F-ACTIN-BINDING PROTEIN; LIKELY ORTHOLOG OF MOUSE SHROOM. [RefSeq;Acc:NM_020859] 0.152828 90 0.385224022 0.396725 SHROOM3
SHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN (CGI-97). [SWISSPROT;Acc:Q9Y3A5] 0.149637 2265 0.222898 0.671325 SBDS
SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN (SRP54). [SWISSPROT;Acc:P13624] 0.241572 2732 0.205477774 1.17566 SRP54
SIGNAL RECOGNITION PARTICLE 68 KDA PROTEIN (SRP68). [SWISSPROT;Acc:Q9UHB9] 0.193159 899 0.259400218 0.744637 SRP68
SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN (SRP9). [SWISSPROT;Acc:P49458] 0.0750779 317 0.291552206 0.257511 SRP9
0.0933039 316 0.291782583 0.319772
SIGNAL RECOGNITION PARTICLE RECEPTOR ALPHA SUBUNIT (SR-ALPHA) (DOCKING PROTEIN ALPHA) (DP-ALPHA). [SWISSPROT;Acc:P08240] 0.411592 2074 0.229287668 1.79509 no value
SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 1-ALPHA/BETA (TRANSCRIPTION FACTOR ISGF-3 COMPONENTS P91/P84). [SWISSPROT;Acc:P42224] 0.331884 858 0.260464605 1.2742 STAT1
SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 3 (ACUTE-PHASE RESPONSE FACTOR). [SWISSPROT;Acc:P40763] 0.333707 856 0.260466441 1.28119 STAT3
SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 4. [SWISSPROT;Acc:Q14765] 0.333006 857 0.260466171 1.2785 STAT4
SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 5A. [SWISSPROT;Acc:P42229] 0.449791 850 0.260555066 1.72628 STAT5A
SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 5B. [SWISSPROT;Acc:P51692] 0.462971 849 0.260563032 1.77681 STAT5B
SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 6 (IL-4 STAT). [SWISSPROT;Acc:P42226] 0.347585 855 0.260480366 1.3344 STAT6
SIGNAL TRANSDUCING ADAPTOR MOLECULE 1; SIGNAL TRANSDUCING ADAPTOR MOLECULE. [RefSeq;Acc:NM_003473] 0.405058 2111 0.228264704 1.77451 STAM
SIGNAL TRANSDUCING ADAPTOR MOLECULE 2; STAM-LIKE PROTEIN CONTAINING SH3 AND ITAM DOMAINS 2. [RefSeq;Acc:NM_005843] 0.337171 2096 0.228463498 1.47582 STAM2
SIGNAL TRANSDUCTION PROTEIN CBL-B (SH3-BINDING PROTEIN CBL-B). [SWISSPROT;Acc:Q13191] 0.502064 93 0.378713293 1.32571 CBLB
SIGNAL-INDUCED PROLIFERATION-ASSOCIATED 1-LIKE 1. [RefSeq;Acc:NM_015556] 0.0671866 688 0.265643682 0.25292 no value
SIMILAR TO ACTIN-RELATED PROTEIN 3-BETA. [SPTREMBL;Acc:Q96BT2] 0.322726 722 0.264677033 1.21932 ACTR3B
SIMILAR TO CG7020 GENE PRODUCT (FRAGMENT). [SPTREMBL;Acc:Q96IB4] 0.465778 2709 0.207346964 2.24637 DIP2B
SIMILAR TO ECOTROPIC VIRAL INTEGRATION SITE 5; NEUROBLASTOMA STAGE 4S GENE. [RefSeq;Acc:NM_145245] 0.0401118 1296 0.245899107 0.163123 EVI5L
SIMILAR TO EXPRESSED SEQUENCE AA415817. [SPTREMBL;Acc:Q8N4Q9] 0.306813 145 0.351374287 0.87318 PDXDC1
SIMILAR TO EXPRESSED SEQUENCE AI415388 (FRAGMENT). [SPTREMBL;Acc:Q8N428] 0.0370824 564 0.270810846 0.136931 GALNTL1

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/