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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measured Gene Rank Hugo description expected final
Results: HTML CSV LaTeX Showing element 2208 to 2257 of 3206 in total
measured
Rank
Hugo
description
expected
final
0.213008 1331 RRP1 NNP-1 PROTEIN (NOVEL NUCLEAR PROTEIN 1) (NUCLEOLAR PROTEIN NOP52) (NOP52) (D21S2056E). [SWISSPROT;Acc:P56182] 0.867932 0.245420148
0.213242 1471 MORF4L2 TRANSCRIPTION FACTOR-LIKE PROTEIN MRGX (MORF-RELATED GENE X PROTEIN) (MORTALITY FACTOR 4-LIKE 2) (MSL3-2 PROTEIN). [SWISSPROT;Acc:Q15014] 0.877587 0.242986735
0.21331 897 VPS18 VACUOLAR PROTEIN SORTING 18 (HVPS18). [SWISSPROT;Acc:Q9P253] 0.821874 0.259541
0.21385 2341 RARS2 ARGINYL-TRNA SYNTHETASE-LIKE; ARGININE-TRNA LIGASE. [RefSeq;Acc:NM_020320] 0.968873 0.220720363
0.214133 2186 ARHGEF7 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7 (PAK-INTERACTING EXCHANGE FACTOR BETA) (BETA-PIX) (COOL-1) (P85). [SWISSPROT;Acc:Q14155] 0.945656 0.226438578
0.214138 2855 AGPAT3 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE GAMMA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 3) (1-AGPAT 3) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-GAMMA) (LPAAT-GAMMA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 3). [SWISSPROT;Acc:Q9NRZ7] 1.12158 0.190925302
0.214269 324 HMG20A HIGH-MOBILITY GROUP 20A. [RefSeq;Acc:NM_018200] 0.744947 0.287629858
0.214312 2508 RSU1 RAS SUPPRESSOR PROTEIN 1 (RSU-1) (RSP-1). [SWISSPROT;Acc:Q15404] 0.997879 0.214767522
0.214359 1844 no value 60S RIBOSOMAL PROTEIN L18A. [SWISSPROT;Acc:Q02543] 0.917867 0.233540371
0.214415 2129 KIAA1432 BA207C16.2 (FRAGMENT). [SPTREMBL;Acc:Q9NQL7] 0.940372 0.22801083
0.214575 1687 PPAT AMIDOPHOSPHORIBOSYLTRANSFERASE PRECURSOR (EC 2.4.2.14) (GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE) (ATASE) (GPAT). [SWISSPROT;Acc:Q06203] 0.901215 0.238095238
0.215243 452 no value "PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 (EC 3.1.3.48) (PROTEIN-TYROSINE PHOSPHATASE 1B) (PTP-1B). [SWISSPROT;Acc:P18031]" 0.779889 0.27599184
0.215454 2338 WRNIP1 WERNER HELICASE INTERACTING PROTEIN ISOFORM 1; PUTATIVE HELICASE RUVBL; WERNER HELICASE INTERACTING PROTEIN. [RefSeq;Acc:NM_020135] 0.975402 0.220887388
0.215654 217 DRAP1 DR1-ASSOCIATED PROTEIN 1; NEGATIVE COFACTOR 2 ALPHA; DR1-ASSOCIATED COREPRESSOR. [RefSeq;Acc:NM_006442] 0.675264 0.319362501
0.215775 1847 SARS2 "SERYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRSMT). [SWISSPROT;Acc:Q9NP81]" 0.924279 0.233452237
0.216085 746 EIF3K EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 11 (EIF-3 P25) (EIF3K) (MUSCLE SPECIFIC GENE M9 PROTEIN) (PTD001) (HSPC029) (ARG134). [SWISSPROT;Acc:Q9UBQ5] 0.816964 0.264497579
0.216233 336 RBBP7 HISTONE ACETYLTRANSFERASE TYPE B SUBUNIT 2 (RETINOBLASTOMA BINDING PROTEIN P46) (RETINOBLASTOMA-BINDING PROTEIN 7) (RBBP-7). [SWISSPROT;Acc:Q16576] 0.758752 0.284985081
0.216511 531 RBM38 RNA-BINDING REGION CONTAINING PROTEIN 1 (HSRNASEB) (SSDNA BINDING PROTEIN SEB4) (CLL-ASSOCIATED ANTIGEN KW-5). [SWISSPROT;Acc:Q9H0Z9] 0.797256 0.271570236
0.2166 1026 TRPC5 SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 5 (TRPC5) (HTRP-5) (HTRP5). [SWISSPROT;Acc:Q9UL62] 0.854644 0.253438859
1027 TBC1D10A EBP50-PDZ INTERACTOR OF 64 KDA (EPI64 PROTEIN). [SWISSPROT;Acc:Q9BXI6]
0.217015 140 GABRA4 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-4 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P48169] 0.617604 0.351382115
0.217355 2962 no value TRANSFORMING PROTEIN N-RAS. [SWISSPROT;Acc:P01111] 1.48707 0.146163261
0.217383 1472 TRANSCRIPTION FACTOR-LIKE PROTEIN MORF4 (MORTALITY FACTOR 4) (CELLULAR SENESCENCE-RELATED PROTEIN 1) (SEN1). [SWISSPROT;Acc:Q9Y690] 0.894645 0.242982412
0.217793 761 DVL1 SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-1 (DISHEVELLED-1) (DSH HOMOLOG 1). [SWISSPROT;Acc:O14640] 0.825859 0.26371693
0.218174 650 MAPK8IP3 C-JUN-AMINO-TERMINAL KINASE INTERACTING PROTEIN 3 (JNK-INTERACTING PROTEIN 3) (JIP-3) (JNK MAP KINASE SCAFFOLD PROTEIN 3) (MITOGEN- ACTIVATED PROTEIN KINASE 8-INTERACTING PROTEIN 3). [SWISSPROT;Acc:Q9UPT6] 0.814576 0.267837501
0.21824 2090 NUPL1 NUCLEOPORIN LIKE 1. [RefSeq;Acc:NM_014089] 0.954199 0.228715394
0.218317 142 GABRA6 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-6 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:Q16445] 0.62131 0.351381758
0.218407 469 TMLHE "TRIMETHYLLYSINE DIOXYGENASE, MITOCHONDRIAL PRECURSOR (EC 1.14.11.8) (EPSILON-TRIMETHYLLYSINE 2-OXOGLUTARATE DIOXYGENASE) (TML-ALPHA- KETOGLUTARATE DIOXYGENASE) (TML HYDROXYLASE) (TML DIOXYGENASE) (TMLD). [SWISSPROT;Acc:Q9NVH6]" 0.794482 0.274904907
0.218499 1796 PDCD5 PROGRAMMED CELL DEATH PROTEIN 5 (TFAR19 PROTEIN) (TF-1 CELL APOPTOSIS RELATED GENE-19 PROTEIN). [SWISSPROT;Acc:O14737] 0.930463 0.234828252
0.218717 2956 ARAF A-RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (A-RAF-1) (PROTO-ONCOGENE PKS). [SWISSPROT;Acc:P10398] 1.48145 0.147637112
0.218752 1600 no value TRANSLIN. [SWISSPROT;Acc:Q15631] 0.911432 0.240009128
0.218789 2211 MLH1 DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1). [SWISSPROT;Acc:P40692] 0.972163 0.225053823
0.21933 1539 no value HISTONE H3.3 (H3.A) (H3.B) (H3.3Q). [SWISSPROT;Acc:P06351] 0.906671 0.241906932
0.219446 139 GABRE GAMMA-AMINOBUTYRIC-ACID RECEPTOR EPSILON SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P78334] 0.624522 0.351382337
0.219758 2955 RAF1 RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (RAF-1) (C-RAF). [SWISSPROT;Acc:P04049] 1.48848 0.147639202
0.219762 368 HNRPH1 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H (HNRNP H). [SWISSPROT;Acc:P31943] 0.785612 0.279733507
0.219925 1894 CKM "CREATINE KINASE, M CHAIN (EC 2.7.3.2) (M-CK). [SWISSPROT;Acc:P06732]" 0.945419 0.232621726
0.22015 2996 RNF25 RING FINGER PROTEIN 25 (EC 6.3.2.-). [SWISSPROT;Acc:Q96BH1] 1.62938 0.135112742
0.220284 706 AOF2 0.830799 0.265147166
0.220469 2536 ODC1 ORNITHINE DECARBOXYLASE (EC 4.1.1.17) (ODC). [SWISSPROT;Acc:P11926] 1.02669 0.214737652
0.221131 245 PRKAG2 "5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-2 SUBUNIT (AMPK GAMMA-2 CHAIN) (AMPK GAMMA2) (H91620P). [SWISSPROT;Acc:Q9UGJ0]" 0.70777 0.312433418
0.221267 2238 no value 0.988036 0.223946293
0.221383 1995 INTEGRAL MEMBRANE PROTEIN CII-3B. [SPTREMBL;Acc:O75609] 0.959291 0.230777731
0.221484 617 PPP3CC "SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, GAMMA ISOFORM (EC 3.1.3.16) (CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, GAMMA ISOFORM) (CALCINEURIN, TESTIS-SPECIFIC CATALYTIC SUBUNIT) (CAM-PRP CATALYTIC SUBUNIT). [SWISSPROT;Acc:P48454]" 0.824699 0.26856344
0.221494 2330 RPS27L RIBOSOMAL PROTEIN S27-LIKE PROTEIN; 40S RIBOSOMAL PROTEIN S27 ISOFORM. [RefSeq;Acc:NM_015920] 1.00105 0.221261675
0.221521 2144 ICT1 IMMATURE COLON CARCINOMA TRANSCRIPT 1 (DIGESTION SUBSTRACTION 1) (DS- 1). [SWISSPROT;Acc:Q14197] 0.972411 0.227805938
0.22158 95 KCNA2 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 2 (POTASSIUM CHANNEL KV1.2) (RBK2) (HBK5) (NGK1) (MK2) (HUKIV). [SWISSPROT;Acc:P16389] 0.589242 0.376042441
0.222111 369 HNRPH2 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H' (HNRNP H') (FTP-3). [SWISSPROT;Acc:P55795] 0.794014 0.279731844
0.222245 1790 ARG1 ARGINASE 1 (EC 3.5.3.1) (LIVER-TYPE ARGINASE). [SWISSPROT;Acc:P05089] 0.945747 0.234994137
0.222313 1858 POLR2G DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB7). [SWISSPROT;Acc:P52433] 0.952373 0.233430599

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/