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

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/