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 Hugo final
Results: HTML CSV LaTeX Showing element 501 to 550 of 3206 in total
description
Rank
measured
expected
Hugo
final
"ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT (MU-ADAPTIN 1) (ADAPTOR PROTEIN COMPLEX AP-1 MU-1 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN MU-1 SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN 1) (CLATHRIN COAT ASSEMBLY PROTEIN A" 1088 0.168157 0.668251 AP1M1 0.251637484
"ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 2 SUBUNIT (MU-ADAPTIN 2) (ADAPTOR PROTEIN COMPLEX AP-1 MU-2 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN MU-2 SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN 2) (AP-MU CHAIN FAMILY MEMBER MU1B)." 1095 0.138969 0.552694 AP1M2 0.251439314
"ADENYLATE CYCLASE, TYPE V (EC 4.6.1.1) (ATP PYROPHOSPHATE-LYASE) (ADENYLYL CYCLASE) (FRAGMENT). [SWISSPROT;Acc:O95622]" 844 0.162988 0.625183 ADCY5 0.260704466
"ADENYLATE CYCLASE, TYPE VI (EC 4.6.1.1) (ATP PYROPHOSPHATE-LYASE) (CA(2+)-INHIBITABLE ADENYLYL CYCLASE). [SWISSPROT;Acc:O43306]" 845 0.198584 0.761721 ADCY6 0.260704379
"ADENYLATE KINASE ISOENZYME 2, MITOCHONDRIAL (EC 2.7.4.3) (ATP-AMP TRANSPHOSPHORYLASE). [SWISSPROT;Acc:P54819]" 1912 0.434898 1.87377 AK2 0.232097856
"ADENYLATE KINASE ISOENZYME 4, MITOCHONDRIAL (EC 2.7.4.3) (ATP-AMP TRANSPHOSPHORYLASE). [SWISSPROT;Acc:P27144]" 1967 0.355425 1.53719 no value 0.231217351
"ADP,ATP CARRIER PROTEIN, FIBROBLAST ISOFORM (ADP/ATP TRANSLOCASE 2) (ADENINE NUCLEOTIDE TRANSLOCATOR 2) (ANT 2). [SWISSPROT;Acc:P05141]" 1692 0.032514 0.136688 SLC25A5 0.237870186
"ADP,ATP CARRIER PROTEIN, HEART/SKELETAL MUSCLE ISOFORM T1 (ADP/ATP TRANSLOCASE 1) (ADENINE NUCLEOTIDE TRANSLOCATOR 1) (ANT 1). [SWISSPROT;Acc:P12235]" 1693 SLC25A4
"ADP,ATP CARRIER PROTEIN, LIVER ISOFORM T2 (ADP/ATP TRANSLOCASE 3) (ADENINE NUCLEOTIDE TRANSLOCATOR 3) (ANT 3). [SWISSPROT;Acc:P12236]" 1696 0.0311972 0.131153 SLC25A6 0.237868749
"ADRENODOXIN, MITOCHONDRIAL PRECURSOR (ADRENAL FERREDOXIN) (HEPATOREDOXIN) (FERREDOXIN 1). [SWISSPROT;Acc:P10109]" 2227 0.42248 1.8831 FDX1 0.22435346
"ALPHA-(1,6)-FUCOSYLTRANSFERASE (EC 2.4.1.68) (GLYCOPROTEIN 6-ALPHA-L- FUCOSYLTRANSFERASE) (GDP-FUCOSE--GLYCOPROTEIN FUCOSYLTRANSFERASE) (GDP-L-FUC:N-ACETYL-BETA-D-GLUCOSAMINIDE ALPHA1,6-FUCOSYLTRANSFERASE) (ALPHA1-6FUCT) (FUCOSYLTRANSFERASE 8). [SW" 991 0.0378287 0.148317 FUT8 0.255053028
"ALPHA-1-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, ACIDIC COMPONENT 1) (PRO-TGF-ALPHA CYTOPLASMIC DOMAIN-INTERACTING PROTEIN 1) (TACIP1) (SYNTROPHIN 1). [SWISSPROT;Acc:Q13424]" 1218 0.0640593 0.258242 SNTA1 0.248059185
"ALPHA-SOLUBLE NSF ATTACHMENT PROTEIN (SNAP-ALPHA) (N-ETHYLMALEIMIDE- SENSITIVE FACTOR ATTACHMENT PROTEIN, ALPHA). [SWISSPROT;Acc:P54920]" 805 0.143723 0.548537 NAPA 0.262011496
"AMINOMETHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.10) (GLYCINE CLEAVAGE SYSTEM T PROTEIN) (GCVT). [SWISSPROT;Acc:P48728]" 2071 0.130784 0.569999 AMT 0.229446017
"ANILLIN, ACTIN BINDING PROTEIN (SCRAPS HOMOLOG, DROSOPHILA); ANILLIN (DROSOPHILA SCRAPS HOMOLOG), ACTIN BINDING PROTEIN. [RefSeq;Acc:NM_018685]" 3202 0.0289077 1.20992 ANLN 0.023892241
"ANKYRIN 2 (BRAIN ANKYRIN) (ANKYRIN B) (ANKYRIN, NONERYTHROID). [SWISSPROT;Acc:Q01484]" 1824 0.038359 0.163741 ANK2 0.234266311
"ARGINASE II, MITOCHONDRIAL PRECURSOR (EC 3.5.3.1) (NON-HEPATIC ARGINASE) (KIDNEY-TYPE ARGINASE). [SWISSPROT;Acc:P78540]" 1786 0.18522 0.787708 ARG2 0.235137894
"ASPARAGINYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.22) (ASPARAGINE-- TRNA LIGASE) (ASNRS). [SWISSPROT;Acc:O43776]" 2752 0.117541 0.576375 NARS 0.203931468
"ATAXIN 2; OLIVOPONTOCEREBELLAR ATAXIA 2, AUTOSOMAL DOMINANT. [RefSeq;Acc:NM_002973]" 2799 0.0572133 0.287777 no value 0.198811232
"ATP SYNTHASE ALPHA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P25705]" 2562 0.383439 1.79234 ATP5A1 0.213932066
"ATP SYNTHASE B CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P24539]" 212 0.155654 0.485577 ATP5F1 0.320554721
"ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P06576]" 2262 0.366428 1.64277 ATP5B 0.223054962
"ATP SYNTHASE COUPLING FACTOR B, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q99766]" 1795 0.0303657 0.129305 ATP5S 0.234837787
"ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P30049]" 2391 0.301597 1.37291 ATP5D 0.219677182
"ATP SYNTHASE F CHAIN, MITOCHONDRIAL (EC 3.6.3.14). [SWISSPROT;Acc:P56134]" 2612 0.0258274 0.122212 ATP5J2 0.211332766
"ATP SYNTHASE GAMMA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P36542]" 2245 0.28274 1.26423 ATP5C1 0.223646014
"ATP SYNTHASE OLIGOMYCIN SENSITIVITY CONFERRAL PROTEIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14) (OSCP). [SWISSPROT;Acc:P48047]" 2246 ATP5O
"ATP-BINDING CASSETTE, SUB-FAMILY C, MEMBER 10; MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 7. [RefSeq;Acc:NM_033450]" 2909 0.0326222 0.187331 ABCC10 0.174142027
"ATP-BINDING CASSETTE, SUB-FAMILY D, MEMBER 3 (70 KDA PEROXISOMAL MEMBRANE PROTEIN) (PMP70). [SWISSPROT;Acc:P28288]" 694 0.0441291 0.166122 ABCD3 0.26564272
"ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:O76031]" 1977 0.139859 0.605241 CLPX 0.231079851
"ATP-DEPENDENT DNA HELICASE II, 70 KDA SUBUNIT (LUPUS KU AUTOANTIGEN PROTEIN P70) (KU70) (70 KDA SUBUNIT OF KU ANTIGEN) (THYROID-LUPUS AUTOANTIGEN) (TLAA) (CTC BOX BINDING FACTOR 75 KDA SUBUNIT) (CTCBF) (CTC75). [SWISSPROT;Acc:P12956]" 1040 0.0397033 0.156754 no value 0.253284127
"ATP-DEPENDENT DNA HELICASE II, 80 KDA SUBUNIT (LUPUS KU AUTOANTIGEN PROTEIN P86) (KU86) (KU80) (86 KDA SUBUNIT OF KU ANTIGEN) (THYROID- LUPUS AUTOANTIGEN) (TLAA) (CTC BOX BINDING FACTOR 85 KDA SUBUNIT) (CTCBF) (CTC85) (NUCLEAR FACTOR IV) (DNA-REPAIR PROTE" 1042 0.114355 0.451492 XRCC5 0.25328245
"ATPASE INHIBITOR, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q9UII2]" 441 0.0602832 0.217862 ATPIF1 0.276703601
"ATPASE, H+ TRANSPORTING, LYSOSOMAL 38KDA, V0 SUBUNIT D ISOFORM 2. [RefSeq;Acc:NM_152565]" 1763 0.33278 1.40872 ATP6V0D2 0.236228633
"ATPASE, H+ TRANSPORTING, LYSOSOMAL V0 SUBUNIT A ISOFORM 4; VACUOLAR PROTON PUMP 116 KDA ACCESSORY SUBUNIT; VACUOLAR PROTON PUMP, SUBUNIT 2; H(+)-TRANSPORTING TWO-SECTOR ATPASE, NONCATALYTIC ACCESSORY PROTEIN 1B; ATPASE, H+ TRANSPORTING, LYSOSOMAL (VACUOLA" 1717 0.224133 0.944489 ATP6V0A4 0.237306099
"AXONEMAL DYNEIN LIGHT INTERMEDIATE POLYPEPTIDE 1 (INNER DYNEIN ARM LIGHT CHAIN, AXONEMAL) (HP28). [SWISSPROT;Acc:O14645]" 2195 0.124723 0.551845 DNALI1 0.226010927
"B-CELL CLL/LYMPHOMA 6, MEMBER B (ZINC FINGER PROTEIN); ZINC FINGER PROTEIN 62. [RefSeq;Acc:NM_181844]" 737 0.0692921 0.261825 BCL6B 0.264650434
"BA138E2.1.2 (FORMIN-BINDING PROTEIN 17 (FBP17), ISOFORM 2). [SPTREMBL;Acc:Q96LH6]" 409 0.404169 1.45394 FNBP1 0.277981897
"BASIC HELIX-LOOP-HELIX DOMAIN CONTAINING, CLASS B, 5; TRINUCLEOTIDE REPEAT CONTAINING 20. [RefSeq;Acc:NM_152414]" 3052 0.090943 0.857352 BHLHB5 0.106074285
"BETA-1,4 MANNOSYLTRANSFERASE. [RefSeq;Acc:NM_019109]" 3126 0.0577935 0.785148 ALG1 0.073608415
"BETA-1-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, BASIC COMPONENT 1) (DAPA1B) (TAX INTERACTION PROTEIN 43) (TIP-43) (SYNTROPHIN 2) (BSYN2). [SWISSPROT;Acc:Q13884]" 1215 0.0802494 0.323509 SNTB1 0.24805925
"BETA-2-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, BASIC COMPONENT 2) (SYNTROPHIN 3) (SNT3) (SYNTROPHIN-LIKE) (SNTL). [SWISSPROT;Acc:Q13425]" 1210 0.0666089 0.26852 SNTB2 0.248059362
"BETA-ARRESTIN 1 (ARRESTIN, BETA 1). [SWISSPROT;Acc:P49407]" 2985 0.282189 2.04196 ARRB1 0.138195165
"BETA-ARRESTIN 2 (ARRESTIN, BETA 2). [SWISSPROT;Acc:P32121]" 2988 0.240182 1.738 ARRB2 0.138194476
"BETA-CAROTENE 15, 15'-DIOXYGENASE; BETA-CAROTENE 15,15'-MONOOXYGENASE. [RefSeq;Acc:NM_017429]" 283 0.0549835 0.182179 BCMO1 0.301810307
"BETA-CAROTENE DIOXYGENASE 2; PUTATIVE B,B-CAROTENE-9',10'-DIOXYGENASE. [RefSeq;Acc:NM_031938]" 294 0.0429558 0.142328 no value 0.301808499
"BETA-SOLUBLE NSF ATTACHMENT PROTEIN (SNAP-BETA) (N-ETHYLMALEIMIDE- SENSITIVE FACTOR ATTACHMENT PROTEIN, BETA). [SWISSPROT;Acc:Q9H115]" 793 0.129493 0.494224 NAPB 0.262012772
"BLOOM'S SYNDROME PROTEIN (EC 3.6.1.-) (RECQ PROTEIN-LIKE 3) (DNA HELICASE, RECQ-LIKE, TYPE 2). [SWISSPROT;Acc:P54132]" 2394 0.106596 0.485769 no value 0.219437634
"BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, CYTOSOLIC (EC 2.6.1.42) (BCAT(C)) (ECA39 PROTEIN). [SWISSPROT;Acc:P54687]" 1461 0.471522 1.94005 BCAT1 0.243046313
"BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.42) (BCAT(M)) (PLACENTAL PROTEIN 18) (PP18). [SWISSPROT;Acc:O15382]" 1452 0.384181 1.57878 BCAT2 0.243340427

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/