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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Hugo measured Gene description expected final Rank
Results: HTML CSV LaTeX Showing element 501 to 550 of 3206 in total
Hugo
measured
description
expected
final
Rank
ARHGAP10 0.0163276 0.0681463 0.23959628 1623
ARHGAP21 0.0500251 RHO-GTPASE ACTIVATING PROTEIN 10. [RefSeq;Acc:NM_020824] 0.180355 0.277370187 426
ARHGAP23 0.0397949 0.143472 0.277370497 424
ARHGAP26 0.0203871 OLIGOPHRENIN-1 LIKE PROTEIN (GTPASE REGULATOR ASSOCIATED WITH FOCAL ADHESION KINASE). [SWISSPROT;Acc:Q9UNA1] 0.0850893 0.239596518 1622
ARHGEF3 0.0223435 "RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 3; RHOGEF PROTEIN; 59.8 KDA PROTEIN; EXCHANGE FACTOR FOUND IN PLATELETS AND LEUKEMIC AND NEURONAL TISSUES, XPLN. [RefSeq;Acc:NM_019555]" 0.0922076 0.242317336 1527
ARHGEF4 0.0362539 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 ISOFORM A; APC-STIMULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR. [RefSeq;Acc:NM_015320] 0.158511 0.228715357 2091
ARHGEF6 0.257131 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 6 (PAK-INTERACTING EXCHANGE FACTOR ALPHA) (ALPHA-PIX) (COOL-2). [SWISSPROT;Acc:Q15052] 1.13453 0.226640988 2181
ARHGEF7 0.214133 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7 (PAK-INTERACTING EXCHANGE FACTOR BETA) (BETA-PIX) (COOL-1) (P85). [SWISSPROT;Acc:Q14155] 0.945656 0.226438578 2186
ARHGEF9 0.0307532 CDC42 GUANINE EXCHANGE FACTOR 9; HPEM-2 COLLYBISTIN. [RefSeq;Acc:NM_015185] 0.13446 0.228716347 2089
ARID1A 0.182783 "SWI/SNF-RELATED, MATRIX-ASSOCIATED, ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY F MEMBER 1 (SWI-SNF COMPLEX PROTEIN P270) (B120). [SWISSPROT;Acc:O14497]" 0.506093 0.361164845 113
ARID1B 0.155731 BRG1-BINDING PROTEIN ELD/OSA1; ELD (EYELID)/OSA PROTEIN. [RefSeq;Acc:NM_020732] 0.431206 0.36115221 115
ARID4B 0.403732 1.64923 0.244800301 1373
ARL1 0.0394801 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1. [SWISSPROT;Acc:P40616] 0.163824 0.240990941 1566
ARL3 0.038359 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 3. [SWISSPROT;Acc:P36405] 0.163741 0.234266311 1822
ARL4A 0.0296714 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 4. [SWISSPROT;Acc:P40617] 0.122715 0.241791142 1549
ARL6IP5 0.104678 CYTOSKELETON RELATED VITAMIN A RESPONSIVE PROTEIN; GLUTAMATE TRANSPORTER EEAC1-ASSOCIATED PROTEIN; DERMAL PAPILLA DERIVED PROTEIN 11; PUTATIVE MAPK ACTIVATING PROTEIN PM27. [RefSeq;Acc:NM_006407] 0.601977 0.173890365 2913
ARMET 0.0869714 ARMET PROTEIN PRECURSOR (ARGININE-RICH PROTEIN). [SWISSPROT;Acc:P55145] 0.403767 0.215399971 2496
ARPC1A 0.355858 ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 1A (SOP2-LIKE PROTEIN). [SWISSPROT;Acc:Q92747] 1.3445 0.264676832 724
ARPC1B 0.317947 ARP2/3 COMPLEX 41 KDA SUBUNIT (P41-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 1B). [SWISSPROT;Acc:O15143] 1.20127 0.264675718 732
ARPC2 0.427564 ARP2/3 COMPLEX 34 KDA SUBUNIT (P34-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 2). [SWISSPROT;Acc:O15144] 1.62441 0.263211874 778
ARPC3 0.392968 ARP2/3 COMPLEX 21 KDA SUBUNIT (P21-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 3). [SWISSPROT;Acc:O15145] 1.48471 0.264676604 725
ARPC5 0.402903 ARP2/3 COMPLEX 16 KDA SUBUNIT (P16-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 5). [SWISSPROT;Acc:O15511] 1.52156 0.264795999 717
ARPC5L 0.424703 1.60405 0.264769178 719
ARRB1 0.282189 "BETA-ARRESTIN 1 (ARRESTIN, BETA 1). [SWISSPROT;Acc:P49407]" 2.04196 0.138195165 2985
ARRB2 0.240182 "BETA-ARRESTIN 2 (ARRESTIN, BETA 2). [SWISSPROT;Acc:P32121]" 1.738 0.138194476 2988
ARRDC2 1.02292 3.93312 0.260078513 879
ARRDC3 0.0467541 0.193844 0.241194466 1562
ARRDC4 0.0442559 0.183485 0.241196283 1561
ASAH1 0.083902 ACID CERAMIDASE PRECURSOR (EC 3.5.1.23) (ACYLSPHINGOSINE DEACYLASE) (N-ACYLSPHINGOSINE AMIDOHYDROLASE) (AC) (PUTATIVE 32 KDA HEART PROTEIN) (PHP32). [SWISSPROT;Acc:Q13510] 0.35015 0.239617307 1618
ASCC1 0.343832 1.3576 0.253264585 1044
ASCC2 0.0336999 ASC-1 COMPLEX SUBUNIT P100. [RefSeq;Acc:NM_032204] 0.139062 0.242337231 1521
ASL 0.255929 ARGININOSUCCINATE LYASE (EC 4.3.2.1) (ARGINOSUCCINASE) (ASAL). [SWISSPROT;Acc:P04424] 1.14373 0.223766973 2243
ASNS 0.0326245 ASPARAGINE SYNTHETASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.4) (GLUTAMINE- DEPENDENT ASPARAGINE SYNTHETASE) (TS11 CELL CYCLE CONTROL PROTEIN). [SWISSPROT;Acc:P08243] 0.137154 0.237867652 1697
ASNSD1 0.0338955 HCV NS3-TRANSACTIVATED PROTEIN 1. [RefSeq;Acc:NM_019048] 0.142498 0.237866496 1699
ASS1 0.161564 ARGININOSUCCINATE SYNTHASE (EC 6.3.4.5) (CITRULLINE--ASPARTATE LIGASE). [SWISSPROT;Acc:P00966] 0.685844 0.235569605 1778
ATAD1 0.153382 0.756695 0.202699899 2756
ATF2 0.673422 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-2 (ACTIVATING TRANSCRIPTION FACTOR 2) (CAMP RESPONSE ELEMENT BINDING PROTEIN CRE- BP1) (HB16). [SWISSPROT;Acc:P15336] 2.49889 0.269488453 586
ATF3 0.101196 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-3 (ACTIVATING TRANSCRIPTION FACTOR 3). [SWISSPROT;Acc:P18847] 0.30217 0.334897574 182
ATF6 0.0417611 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-6 ALPHA (ACTIVATING TRANSCRIPTION FACTOR 6 ALPHA) (ATF6-ALPHA). [SWISSPROT;Acc:P18850] 0.170257 0.24528272 1343
ATF7 0.574984 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-7 (ACTIVATING TRANSCRIPTION FACTOR 7) (TRANSCRIPTION FACTOR ATF-A). [SWISSPROT;Acc:P17544] 2.13394 0.269447126 587
ATG12 0.196655 AUTOPHAGY PROTEIN 12-LIKE (APG12-LIKE). [SWISSPROT;Acc:O94817] 0.876663 0.224322231 2229
ATG16L1 0.515003 1.71949 0.299509157 302
ATG16L2 0.329649 1.10466 0.298416707 305
ATG3 0.206188 APG3P; PC3-96 PROTEIN. [RefSeq;Acc:NM_022488] 1.59883 0.128961803 3000
ATG4A 0.156084 CYSTEINE ENDOPEPTIDASE AUT-LIKE 2 ISOFORM A; AUTOPHAGY-RELATED CYSTEINE ENDOPEPTIDASE 2; AUTOPHAGIN 2. [RefSeq;Acc:NM_052936] 1.50787 0.103512902 3067
ATG4B 0.126175 CYSTEINE ENDOPEPTIDASE AUT-LIKE ISOFORM B. [RefSeq;Acc:NM_178326] 1.21767 0.103620028 3064
ATG5 0.40611 AUTOPHAGY PROTEIN 5-LIKE (APG5-LIKE) (APOPTOSIS-SPECIFIC PROTEIN). [SWISSPROT;Acc:Q9H1Y0] 1.51635 0.267820754 653
ATIC 0.100408 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] 0.416 0.241365385 1553
ATN1 0.13427 ATROPHIN-1 (DENTATORUBRAL-PALLIDOLUYSIAN ATROPHY PROTEIN). [SWISSPROT;Acc:P54259] 0.484077 0.277373228 417
ATP11A 0.0225037 POTENTIAL PHOSPHOLIPID-TRANSPORTING ATPASE IH (EC 3.6.3.1) (ATPASE CLASS I TYPE 11A) (ATPASE IS). [SWISSPROT;Acc:P98196] 0.0892747 0.252072536 1083

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/