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